Immunoglobulin Chimeric Monomer-Dimer Hybrids

ABSTRACT

The invention relates to a chimeric monomer-dimer hybrid protein wherein said protein comprises a first and a second polypeptide chain, said first polypeptide chain comprising at least a portion of an immunoglobulin constant region and a biologically active molecule, and said second polypeptide chain comprising at least a portion of an immunoglobulin constant region without the biologically active molecule of the first chain. The invention also relates to methods of using and methods of making the chimeric monomer-dimer hybrid protein of the invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser.No. 12/952,551, filed Nov. 23, 2010, which is a divisional applicationof U.S. application Ser. No. 11/588,431, filed Oct. 27, 2006 and issuedJan. 4, 2011 as U.S. Pat. No. 7,862,820, which is a continuationapplication of U.S. application Ser. No. 10/841,250, filed May 6, 2004and issued Jul. 29, 2008 as U.S. Pat. No. 7,404,956, which claimspriority to U.S. Provisional Appl. No. 60/469,600 filed May 6, 2003,U.S. Provisional Appl. No. 60/487,964 filed Jul. 17, 2003, and U.S.Provisional Appl. No. 60/539,207 filed Jan. 26, 2004, all of which areincorporated by reference in their entirety. The U.S. application Ser.No. 10/842,054 nonprovisional application entitled Methods forChemically Synthesizing Immunoglobulin Chimeric Proteins, filedconcurrently on May 6, 2004, is incorporated by reference.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing (Name:SequenceListing.txt, Size: 87,668 bytes; and Date of Creation: Jan. 10,2013) filed with the application is incorporated by reference in itsentirety.

FIELD OF THE INVENTION

The invention relates generally to therapeutic chimeric proteins,comprised of two polypeptide chains, wherein the first chain iscomprised of a therapeutic biologically active molecule and the secondchain is not comprised of the therapeutic biologically active moleculeof the first chain. More specifically, the invention relates to chimericproteins, comprised of two polypeptide chains, wherein both chains arecomprised of at least a portion of an immunoglobulin constant regionwherein the first chain is modified to further comprise a biologicallyactive molecule, and the second chain is not so modified. The invention,thus relates to a chimeric protein that is a monomer-dimer hybrid, i.e.,a chimeric protein having a dimeric aspect and a monomeric aspect,wherein the dimeric aspect relates to the fact that it is comprised oftwo polypeptide chains each comprised of a portion of an immunoglobulinconstant region, and wherein the monomeric aspect relates to the factthat only one of the two chains is comprised of a therapeuticbiologically active molecule. FIG. 1 illustrates one example of amonomer-dimer hybrid wherein the biologically active molecule iserythropoietin (EPO) and the portion of an immunoglobulin constantregion is an IgG Fc region.

BACKGROUND OF THE INVENTION

Immunoglobulins are comprised of four polypeptide chains, two heavychains and two light chains, which associate via disulfide bonds to formtetramers. Each chain is further comprised of one variable region andone constant region. The variable regions mediate antigen recognitionand binding, while the constant regions, particularly the heavy chainconstant regions, mediate a variety of effector functions, e.g.,complement binding and Fc receptor binding (see, e.g., U.S. Pat. Nos.6,086,875; 5,624,821; 5,116,964).

The constant region is further comprised of domains denoted CH (constantheavy) domains (CHI, CH2, etc.). Depending on the isotype, (i.e. IgG,IgM, IgA IgD, IgE) the constant region can be comprised of three or fourCH domains. Some isotypes (e.g. IgG) constant regions also contain ahinge region Janeway et al. 2001, Immunobiology, Garland Publishing,N.Y., N.Y.

The creation of chimeric proteins comprised of immunoglobulin constantregions linked to a protein of interest, or fragment thereof, has beendescribed (see, e.g., U.S. Pat. Nos. 5,480,981 and 5,808,029; Gascoigneet al. 1987, Proc. Natl. Acad. Sci. USA 84:2936; Capon et al. 1989,Nature 337:525; Traunecker et al. 1989, Nature 339:68; Zettmeissl et al.1990, DNA Cell Biol. USA 9:347; Byrn et al. 1990, Nature 344:667; Watsonet al. 1990, J. Cell Biol. 110:2221; Watson et al. 1991, Nature 349:164;Aruffo et al. 1990, Cell 61:1303; Linsley et al. 1991, J. Exp. Med.173:721; Linsley et al. 1991, J. Exp. Med. 174:561; Stamenkovic et al.,1991, Cell 66:1133; Ashkenazi et al. 1991, Proc. Natl. Acad. Sci. USA88:10535; Lesslauer et al. 1991, Eur. J. Immunol. 27:2883; Peppel et al.1991, J. Exp. Med. 174:1483; Bennett et al. 1991, J. Biol. Chem.266:23060; Kurschner et al. 1992, J. Biol. Chem. 267:9354; Chalupny etal. 1992, Proc. Natl. Acad. Sci. USA 89:10360; Ridgway and Gorman, 1991,J. Cell Biol. 115, Abstract No. 1448; Zheng et al. 1995, J. Immun.154:5590). These molecules usually possess both the biological activityassociated with the linked molecule of interest as well as the effectorfunction, or some other desired characteristic associated with theimmunoglobulin constant region (e.g. biological stability, cellularsecretion).

The Fc portion of an immunoglobulin constant region, depending on theimmunoglobulin isotype can include the CH2, CH3, and CH4 domains, aswell as the hinge region. Chimeric proteins comprising an Fc portion ofan immunoglobulin bestow several desirable properties on a chimericprotein including increased stability, increased serum half life (seeCapon et al. 1989, Nature 337:525) as well as binding to Fc receptorssuch as the neonatal Fc receptor (FcRn) (U.S. Pat. Nos. 6,086,875,6,485,726, 6,030,613; WO 03/077834; U52003-0235536A1).

FcRn is active in adult epithelial tissue and expressed in the lumen ofthe intestines, pulmonary airways, nasal surfaces, vaginal surfaces,colon and rectal surfaces (U.S. Pat. No. 6,485,726). Chimeric proteinscomprised of FcRn binding partners (e.g. IgG, Fc fragments) can beeffectively shuttled across epithelial barriers by FcRn, thus providinga non-invasive means to systemically administer a desired therapeuticmolecule. Additionally, chimeric proteins comprising an FcRn bindingpartner are endocytosed by cells expressing the FcRn. But instead ofbeing marked for degradation, these chimeric proteins are recycled outinto circulation again, thus increasing the in vivo half life of theseproteins.

Portions of immunoglobulin constant regions, e.g., FcRn binding partnerstypically associate, via disulfide bonds and other non-specificinteractions, with one another to form dimers and higher ordermultimers. The instant invention is based in part upon the surprisingdiscovery that transcytosis of chimeric proteins comprised of FcRnbinding partners appears to be limited by the molecular weight of thechimeric protein, with higher molecular weight species being transportedless efficiently.

Chimeric proteins comprised of biologically active molecules, onceadministered, typically will interact with a target molecule or cell.The instant invention is further based in part upon the surprisingdiscovery that monomer-dimer hybrids, with one biologically activemolecule, but two portions of an immunoglobulin constant region, e.g.,two FcRn binding partners, function and can be transported moreeffectively than homodimers, also referred to herein simply as “dimers”or higher order multimers with two or more copies of the biologicallyactive molecule. This is due in part to the fact that chimeric proteins,comprised of two or more biologically active molecules, which exist asdimers and higher order multimers, can be sterically hindered frominteracting with their target molecule or cell, due to the presence ofthe two or more biologically active molecules in close proximity to oneanother and that the biologically active molecule can have a highaffinity for itself.

Accordingly one aspect of the invention provides chimeric proteinscomprised of a biologically active molecule that is transported acrossthe epithelium barrier. An additional aspect of the invention provideschimeric proteins comprised of at least one biologically active moleculethat is able to interact with its target molecule or cell with little orno steric hindrance or self aggregation.

The aspects of the invention provide for chimeric proteins comprising afirst and second polypeptide chain, the first chain comprising at leasta portion of immunoglobulin constant region, wherein the portion of animmunoglobulin constant region has been modified to include abiologically active molecule and the second chain comprising at least aportion of immunoglobulin constant region, wherein the portion of animmunoglobulin constant region has not been so modified to include thebiologically active molecule of the first chain.

SUMMARY OF THE INVENTION

The invention relates to a chimeric protein comprising one biologicallyactive molecule and two molecules of at least a portion of animmunoglobulin constant region. The chimeric protein is capable ofinteracting with a target molecule or cell with less steric hindrancecompared to a chimeric protein comprised of at least two biologicallyactive molecules and at least a portion of two immunoglobulin constantregions. The invention also relates to a chimeric protein comprising atleast one biologically active molecule and two molecules of at least aportion of an immunoglobulin constant region that is transported acrossan epithelium barrier more efficiently than a corresponding homodimer,i.e., wherein both chains are linked to the same biologically activemolecule. The invention, thus relates to a chimeric protein comprising afirst and a second polypeptide chain linked together, wherein said firstchain comprises a biologically active molecule and at least a portion ofan immunoglobulin constant region, and said second chain comprises atleast a portion of an immunoglobulin constant region, but noimmunoglobulin variable region and without any biologically activemolecule attached.

The invention relates to a chimeric protein comprising a first and asecond polypeptide chain linked together, wherein said first chaincomprises a biologically active molecule and at least a portion of animmunoglobulin constant region, and said second chain comprises at leasta portion of an immunoglobulin constant region without an immunoglobulinvariable region or any biologically active molecule and wherein saidsecond chain is not covalently bonded to any molecule having a molecularweight greater than 1 kD, 2 kD, 5 kD, 10 kD, or 20 kD. In oneembodiment, the second chain is not covalently bonded to any moleculehaving a molecular weight greater than 0-2 kD. In one embodiment, thesecond chain is not covalently bonded to any molecule having a molecularweight greater than 5-10 kD. In one embodiment, the second chain is notcovalently bonded to any molecule having a molecular weight greater than15-20 kD.

The invention relates to a chimeric protein comprising a first and asecond polypeptide chain linked together, wherein said first chaincomprises a biologically active molecule and at least a portion of animmunoglobulin constant region, and said second chain comprises at leasta portion of an immunoglobulin constant region not covalently linked toany other molecule except the portion of an immunoglobulin of said firstpolypeptide chain.

The invention relates to a chimeric protein comprising a first and asecond polypeptide chain linked together, wherein said first chaincomprises a biologically active molecule and at least a portion of animmunoglobulin constant region, and said second chain consists of atleast a portion of an immunoglobulin constant region and optionally anaffinity tag.

The invention relates to a chimeric protein comprising a first and asecond polypeptide chain linked together, wherein said first chaincomprises a biologically active molecule and at least a portion of animmunoglobulin constant region, and said second chain consistsessentially of at least a portion of an immunoglobulin constant regionand optionally an affinity tag.

The invention relates to a chimeric protein comprising a first and asecond polypeptide chain linked together, wherein said first chaincomprises a biologically active molecule and at least a portion of animmunoglobulin constant region, and said second chain comprises at leasta portion of an immunoglobulin constant region without an immunoglobulinvariable region or any biologically active molecule and optionally amolecule with a molecular weight less than 10 kD, 5 kD, 2 kD or 1 kD. Inone embodiment, the second chain comprises a molecule less than 15-20kD. In one embodiment, the second chain comprises a molecule less than5-10 kD. In one embodiment, the second chain comprises a molecule lessthan 1-2 kD.

The invention relates to a chimeric protein comprising a first andsecond polypeptide chain, wherein said first chain comprises abiologically active molecule, at least a portion of an immunoglobulinconstant region, and at least a first domain, said first domain havingat least one specific binding partner, and wherein said second chaincomprises at least a portion of an immunoglobulin constant region, andat least a second domain, wherein said second domain is a specificbinding partner of said first domain, without any immunoglobulinvariable region or a biologically active molecule.

The invention relates to a method of making a chimeric proteincomprising a first and second polypeptide chain, wherein the firstpolypeptide chain and the second polypeptide chain are not the same,said method comprising transfecting a cell with a first DNA constructcomprising a DNA molecule encoding a first polypeptide chain comprisinga biologically active molecule and at least a portion of animmunoglobulin constant region and optionally a linker, and a second DNAconstruct comprising a DNA molecule encoding a second polypeptide chaincomprising at least a portion of an immunoglobulin constant regionwithout any biologically active molecule or an immunoglobulin variableregion, and optionally a linker, culturing the cells under conditionssuch that the polypeptide chain encoded by the first DNA construct isexpressed and the polypeptide chain encoded by the second DNA constructis expressed and isolating monomer-dimer hybrids comprised of thepolypeptide chain encoded by the first DNA construct and the polypeptidechain encoded by the second DNA construct.

The invention relates to a method of making a chimeric proteincomprising a first and second polypeptide chain, wherein the firstpolypeptide chain and the second polypeptide chain are not the same, andwherein said first polypeptide chain comprises a biologically activemolecule, at least a portion of an immunoglobulin constant region, andat least a first domain, said first domain, having at least one specificbinding partner, and wherein said second polypeptide chain comprises atleast a portion of an immunoglobulin constant region and a seconddomain, wherein said second domain, is a specific binding partner ofsaid first domain, without any biologically active molecule or animmunoglobulin variable region, said method comprising transfecting acell with a first DNA construct comprising a DNA molecule encoding saidfirst polypeptide chain and a second DNA construct comprising a DNAmolecule encoding, said second polypeptide chain, culturing the cellsunder conditions such that the polypeptide chain encoded by the firstDNA construct is expressed and the polypeptide chain encoded by thesecond DNA construct is expressed and isolating monomer-dimer hybridscomprised of the polypeptide chain encoded by the first DNA constructand polypeptide chain encoded by the second DNA construct.

The invention relates to a method of making a chimeric protein of theinvention said method comprising transfecting a cell with a first DNAconstruct comprising a DNA molecule encoding a first polypeptide chaincomprising a biologically active molecule and at least a portion of animmunoglobulin constant region and optionally a linker, culturing thecell under conditions such that the polypeptide chain encoded by thefirst DNA construct is expressed, isolating the polypeptide chainencoded by the first DNA construct and transfecting a cell with a secondDNA construct comprising a DNA molecule encoding a second polypeptidechain comprising at least a portion of an immunoglobulin constant regionwithout any biologically active molecule or immunoglobulin variableregion, culturing the cell under conditions such that the polypeptidechain encoded by the second DNA construct is expressed, isolating thepolypeptide chain, encoded by the second DNA construct, combining thepolypeptide chain, encoded by the first DNA construct and thepolypeptide chain encoded by the second DNA construct under conditionssuch that monomer-dimer hybrids comprising the polypeptide chain encodedby the first DNA construct and the polypeptide chain encoded by thesecond DNA construct form, and isolating said monomer-dimer hybrids.

The invention relates to a method of making a chimeric proteincomprising a first and second polypeptide chain, wherein the firstpolypeptide chain and the second polypeptide chain are not the same,said method comprising transfecting a cell with a DNA constructcomprising a DNA molecule encoding a polypeptide chain comprising atleast a portion of an immunoglobulin constant region, culturing thecells under conditions such that the polypeptide chain encoded by theDNA construct is expressed with an N terminal cysteine such that dimersof the polypeptide chain form and isolating dimers comprised of twocopies of the polypeptide chain encoded by the DNA construct andchemically reacting the isolated dimers with a biologically activemolecule, wherein said biologically active molecule has a C terminusthioester, under conditions such that the biologically active moleculereacts predominantly with only one polypeptide chain of the dimerthereby forming a monomer-dimer hybrid.

The invention relates to a method of making a chimeric proteincomprising a first and second polypeptide chain, wherein the firstpolypeptide chain and the second polypeptide chain are not the same,said method comprising transfecting a cell with a DNA constructcomprising a DNA molecule encoding a polypeptide chain comprising atleast a portion of an immunoglobulin constant region, culturing thecells under conditions such that the polypeptide chain encoded by theDNA construct is expressed with an N terminal cysteine such that dimersof the polypeptide chains form, and isolating dimers comprised of twocopies of the polypeptide chain encoded by the DNA construct, andchemically reacting the isolated dimers with a biologically activemolecule, wherein said biologically active molecule has a C terminusthioester, such that the biologically active molecule is linked to eachchain of the dimer, denaturing the dimer comprised of the portion of theimmunoglobulin linked to the biologically active molecule such thatmonomeric chains form, combining the monomeric chains with a polypeptidechain comprising at least a portion of an immunoglobulin constant regionwithout a biologically active molecule linked to it, such thatmonomer-dimer hybrids form, and isolating the monomer-dimer hybrids.

The invention relates to a method of making a chimeric proteincomprising a first and second polypeptide chain, wherein the firstpolypeptide chain and the second polypeptide chain are not the same,said method comprising transfecting a cell with a DNA constructcomprising a DNA molecule encoding a polypeptide chain comprising atleast a portion of an immunoglobulin constant region, culturing thecells under conditions such that the polypeptide chain encoded by theDNA construct is expressed as a mixture of two polypeptide chains,wherein the mixture comprises a polypeptide with an N terminal cysteine,and a polypeptide with a cysteine in close proximity to the N terminus,isolating dimers comprised of the mixture of polypeptide chains encodedby the DNA construct and chemically reacting the isolated dimers with abiologically active molecule, wherein said biologically active moleculehas an active thioester, such that at least some monomer-dimer hybridforms and isolating the monomer-dimer hybrid from said mixture.

The invention relates to a method of treating a disease or conditioncomprising administering a chimeric protein of the invention therebytreating the disease or condition.

Additional objects and advantages of the invention will be set forth inpart in the description which follows, and in part will be obvious fromthe description, or may be learned by practice of the invention. Theobjects and advantages of the invention will be realized and attained bymeans of the elements and combinations particularly pointed out in theappended claims.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the invention, as claimed.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic diagram comparing the structure of an EPO-Fchomodimer, or dimer, and the structure of an Epo-FC monomer-dimerhybrid.

FIG. 2 a is the amino acid sequence of the chimeric protein FactorVII-Fc (SEQ ID NO: 6). Included in the sequence is the signal peptide(underlined), which is cleaved by the cell and the propeptide (bold),which is recognized by the vitamin K-dependent γ carboxylase whichmodifies the Factor VII to achieve full activity. The sequence issubsequently cleaved by PACE to yield Factor VII-Fc.

FIG. 2 b is the amino acid sequence of the chimeric protein Factor IX-Fc(SEQ ID NO: 8). Included in the sequence is the signal peptide(underlined) which is cleaved by the cell and the propeptide (bold)which is recognized by the vitamin K-dependent γ carboxylase whichmodifies the Factor IX to achieve full activity. The sequence issubsequently cleaved by PACE to yield Factor IX-Fc.

FIG. 2 c is the amino acid sequence of the chimeric protein IFNα-Fc (SEQID NO: 10). Included in the sequence is the signal peptide (underlined),which is cleaved by the cell resulting in the mature IFNα-Fc.

FIG. 2 d is the amino acid sequence of the chimeric protein IFNα-Fc Δlinker (SEQ ID NO: 12). Included in the sequence is the signal peptide(underlined) which is cleaved by the cell resulting in the matureIFNα-Fc Δ linker.

FIG. 2 e is the amino acid sequence of the chimeric protein Flag-Fc (SEQID NO: 14). Included in the sequence is the signal peptide (underlined),which is cleaved by the cell resulting in the mature Flag-Fc.

FIG. 2 f is the amino acid sequence of the chimeric protein Epo-CCA-Fc(SEQ ID NO: 16). Included in the sequence is the signal peptide(underlined), which is cleaved by the cell resulting in the matureEpo-CCA-Fc. Also shown in bold is the acidic coiled coil domain.

FIG. 2 g is the amino acid sequence of the chimeric protein CCB-Fc (SEQID NO: 18). Included in the sequence is the signal peptide (underlined),which is cleaved by the cell resulting in the mature CCB-Fc. Also shownin bold is the basic coiled coil domain.

FIG. 2 h is the amino acid sequence of the chimeric protein Cys-Fc (SEQID NO: 20). Included in the sequence is the signal peptide (underlined),which is cleaved by the cell resulting in the mature Cys-Fc. When thissequence is produced in CHO cells a percentage of the molecules areincorrectly cleaved by the signal peptidase such that two extra aminoacids are left on the N terminus, thus preventing the linkage of abiologically active molecule with a C terminal thioester (e.g., vianative ligation). When these improperly cleaved species dimerize withthe properly cleaved Cys-Fc and are subsequently reacted withbiologically active molecules with C terminal thioesters, monomer-dimerhybrids form.

FIG. 2 i is the amino acid sequence of the chimeric protein IFNα-GS15-Fc(SEQ ID NO: 22). Included in the sequence is the signal peptide(underlined) which is cleaved by the cell resulting in the matureIFNα-GS15-Fc.

FIG. 2 j is the amino acid sequence of the chimeric protein Epo-Fc (SEQID NO: 24). Included in the sequence is the signal peptide (underlined),which is cleaved by the cell resulting in the mature Epo-Fc. Also shownin bold is the 8 amino acid linker.

FIG. 3 a is the nucleic acid sequence of the chimeric protein FactorVII-Fc (SEQ ID NO: 7). Included in the sequence is the signal peptide(underlined) and the propeptide (bold) which is recognized by thevitamin K-dependent γ carboxylase which modifies the Factor VII toachieve full activity. The translated sequence is subsequently cleavedby PACE to yield mature Factor VII-Fc.

FIG. 3 b is the nucleic acid sequence of the chimeric protein FactorIX-Fc (SEQ ID NO: 9). Included in the sequence is the signal peptide(underlined) and the propeptide (bold) which is recognized by thevitamin K-dependent γ carboxylase which modifies the Factor IX toachieve full activity. The translated sequence is subsequently cleavedby PACE to yield mature Factor IX-Fc.

FIG. 3 c is the nucleic acid sequence of the chimeric protein IFNα-Fc(SEQ ID NO: 11). Included in the sequence is the signal peptide(underlined), which is cleaved by the cell after translation resultingin the mature IFNα-Fc.

FIG. 3 d is the nucleic acid sequence of the chimeric protein IFNα-Fc Δlinker (SEQ ID NO: 13). Included in the sequence is the signal peptide(underlined) which is cleaved by the cell after translation resulting inthe mature IFNα-Fc Δ linker.

FIG. 3 e is the amino acid sequence of the chimeric protein Flag-Fc (SEQID NO: 15). Included in the sequence is the signal peptide (underlined),which is cleaved by the cell after translation resulting in the matureFlag-Fc.

FIG. 3 f is the nucleic acid sequence of the chimeric protein Epo-CCA-Fc(SEQ ID NO: 17). Included in the sequence is the signal peptide(underlined), which is cleaved by the cell after translation resultingin the mature Epo-CCA-Fc. Also shown in bold is the acidic coiled coildomain.

FIG. 3 g is the nucleic acid sequence of the chimeric protein CCB-Fc(SEQ ID NO: 19). Included in the sequence is the signal peptide(underlined), which is cleaved by the cell after translation resultingin the mature CCB-Fc. Also shown in bold is the basic coiled coildomain.

FIG. 3 h is the nucleic acid sequence of the chimeric protein Cys-Fc(SEQ ID NO: 21). Included in the sequence is the signal peptide(underlined), which is cleaved by the cell after translation resultingin the mature Cys-Fc.

FIG. 3 i is the nucleic acid sequence of the chimeric proteinIFNa-GS15-Fc (SEQ ID NO: 23). Included in the sequence is the signalpeptide (underlined) which is cleaved by the cell after translationresulting in the mature IFNα-GS15-Fc.

FIG. 3 j is the nucleic acid sequence of the chimeric protein Epo-Fc(SEQ ID NO: 25). Included in the sequence is the signal peptide(underlined), which is cleaved by the cell after translation resultingin the mature Epo-Fc. Also shown in bold is a nucleic acid sequenceencoding the 8 amino acid linker.

FIG. 4 demonstrates ways to form monomer-dimer hybrids through nativeligation. SVGCPPC, VGCPPC, STGCPPC and CPPC disclosed as SEQ ID NOS87-90, respectively.

FIG. 5 a shows the amino acid sequence of Fc MESNA (SEQ ID NO:4).

FIG. 5 b shows the DNA sequence of Fc MESNA (SEQ ID NO:5).

FIG. 6 compares antiviral activity of IFNα homo-dimer (i.e. comprised of2 IFNα molecules) with an IFNα monomer-dimer hybrid (i.e. comprised of 1IFNα molecule).

FIG. 7 is a comparison of clotting activity of a chimeric monomer-dimerhybrid Factor VIIa-Fc (one Factor VII molecule) and a chimeric homodimerFactor VIIa-Fc (two Factor VII molecules).

FIG. 8 compares oral dosing in neonatal rats of a chimeric monomer-dimerhybrid Factor VIIa-Fc (one Factor VII molecule) and a chimeric homodimerFactor VIIa-Fc (two Factor VII molecules).

FIG. 9 compares oral dosing in neonatal rats of a chimeric monomer-dimerhybrid Factor IX-Fc (one Factor IX molecule) with a chimeric homodimer.

FIG. 10 is a time course study comparing a chimeric monomer-dimer hybridFactor IX-Fc (one Factor IX molecule) administered orally to neonatalrats with an orally administered chimeric homodimer.

FIG. 11 demonstrates pharmokinetics of Epo-Fc dimer compared to Epo-Fcmonomer-dimer hybrid in cynomolgus monkeys after a single pulmonarydose.

FIG. 12 compares serum concentration in monkeys of subcutaneouslyadministered Epo-Fc monomer-dimer hybrid with subcutaneouslyadministered Aranesp® (darbepoetin alfa).

FIG. 13 compares serum concentration in monkeys of intravenouslyadministered Epo-Fc monomer-dimer hybrid with intravenously administeredAranesp® (darbepoetin alfa) and Epogen® (epoetin alfa).

FIG. 14 shows a trace from a Mimetic Red 2™ column (ProMeticLifeSciences, Inc., Wayne, N.J.) and an SDS-PAGE of fractions from thecolumn containing EpoFc monomer-dimer hybrid, EpoFc dimer, and Fc. EpoFcmonomer-dimer hybrid is found in fractions 11, 12, 13, and 14. EpoFcdimer is found in fraction 18. Fc is found in fractions ½.

FIG. 15 shows the pharmacokinetics of IFNβFc with an 8 amino acid linkerin cynomolgus monkeys after a single pulmonary dose.

FIG. 16 shows neopterin stimulation in response to the IFNβ-Fc homodimerand the IFNβ-Fc N297A monomer-dimer hybrid in cynomolgus monkeys.

FIG. 17 a shows the nucleotide sequence of interferon β-Fc (SEQ ID NO:98);

FIG. 17 b shows the amino acid sequence of interferon β-Fc (SEQ ID NO:99).

FIG. 18 a shows the amino acid sequence of T20 (SEQ ID NO: 1); FIG. 18 bshows the amino acid sequence of T21 (SEQ ID NO: 2) and FIG. 18 c showsthe amino acid sequence of T1249 (SEQ ID NO: 3).

DESCRIPTION OF THE EMBODIMENTS A. Definitions

Affinity tag, as used herein, means a molecule attached to a secondmolecule of interest, capable of interacting with a specific bindingpartner for the purpose of isolating or identifying said second moleculeof interest.

Analogs of chimeric proteins of the invention, or proteins or peptidessubstantially identical to the chimeric proteins of the invention, asused herein, means that a relevant amino acid sequence of a protein or apeptide is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%identical to a given sequence. By way of example, such sequences may bevariants derived from various species, or they may be derived from thegiven sequence by truncation, deletion, amino acid substitution oraddition. Percent identity between two amino acid sequences isdetermined by standard alignment algorithms such as, for example, BasicLocal Alignment Tool (BLAST) described in Altschul et al. 1990, J. Mol.Biol., 215:403-410, the algorithm of Needleman et al. 1970, J. Mol.Biol., 48:444-453; the algorithm of Meyers et al. 1988, Comput. Appi.Biosci., 4:11-17; or Tatusova et al. 1999, FEMS Microbiol. Lett.,174:247-250, etc. Such algorithms are incorporated into the BLASTN,BLASTP and “BLAST 2 Sequences” programs (seewww.ncbi.nlm.nih.gov/BLAST). When utilizing such programs, the defaultparameters can be used. For example, for nucleotide sequences thefollowing settings can be used for “BLAST 2 Sequences”: program BLASTN,reward for match 2, penalty for mismatch −2, open gap and extension gappenalties 5 and 2 respectively, gap x_dropoff 50, expect 10, word size11, filter ON. For amino acid sequences the following settings can beused for “BLAST 2 Sequences”: program BLASTP, matrix BLOSUM62, open gapand extension gap penalties 11 and 1 respectively, gap x_dropoff 50,expect 10, word size 3, filter ON.

Bioavailability, as used herein, means the extent and rate at which asubstance is absorbed into a living system or is made available at thesite of physiological activity.

Biologically active molecule, as used herein, means a non-immunoglobulinmolecule or fragment thereof, capable of treating a disease or conditionor localizing or targeting a molecule to a site of a disease orcondition in the body by performing a function or an action, orstimulating or responding to a function, an action or a reaction, in abiological context (e.g. in an organism, a cell, or an in vitro modelthereof). Biologically active molecules may comprise at least one ofpolypeptides, nucleic acids, small molecules such as small organic orinorganic molecules.

A chimeric protein, as used herein, refers to any protein comprised of afirst amino acid sequence derived from a first source, bonded,covalently or non-covalently, to a second amino acid sequence derivedfrom a second source, wherein the first and second source are not thesame. A first source and a second source that are not the same caninclude two different biological entities, or two different proteinsfrom the same biological entity, or a biological entity and anon-biological entity. A chimeric protein can include for example, aprotein derived from at least 2 different biological sources. Abiological source can include any non-synthetically produced nucleicacid or amino acid sequence (e.g. a genomic or cDNA sequence, a plasmidor viral vector, a native virion or a mutant or analog, as furtherdescribed herein, of any of the above). A synthetic source can include aprotein or nucleic acid sequence produced chemically and not by abiological system (e.g. solid phase synthesis of amino acid sequences).A chimeric protein can also include a protein derived from at least 2different synthetic sources or a protein derived from at least onebiological source and at least one synthetic source. A chimeric proteinmay also comprise a first amino acid sequence derived from a firstsource, covalently or non-covalently linked to a nucleic acid, derivedfrom any source or a small organic or inorganic molecule derived fromany source. The chimeric protein may comprise a linker molecule betweenthe first and second amino acid sequence or between the first amino acidsequence and the nucleic acid, or between the first amino acid sequenceand the small organic or inorganic molecule.

Clotting factor, as used herein, means any molecule, or analog thereof,naturally occurring or recombinantly produced which prevents ordecreases the duration of a bleeding episode in a subject with ahemostatic disorder. In other words, it means any molecule havingclotting activity.

Clotting activity, as used herein, means the ability to participate in acascade of biochemical reactions that culminates in the formation of afibrin clot and/or reduces the severity, duration or frequency ofhemorrhage or bleeding episode.

Dimer as used herein refers to a chimeric protein comprising a first andsecond polypeptide chain, wherein the first and second chains bothcomprise a biologically active molecule, and at least a portion of animmunoglobulin constant region. A homodimer refers to a dimer where bothbiologically active molecules are the same.

Dimerically linked monomer-dimer hybrid refers to a chimeric proteincomprised of at least a portion of an immunoglobulin constant region,e.g. an Fc fragment of an immunoglobulin, a biologically active moleculeand a linker which links the two together such that one biologicallyactive molecule is bound to 2 polypeptide chains, each comprising aportion of an immunoglobulin constant region. FIG. 4 shows an example ofa dimerically linked monomer-dimer hybrid.

DNA construct, as used herein, means a DNA molecule, or a clone of sucha molecule, either single- or double-stranded that has been modifiedthrough human intervention to contain segments of DNA combined in amanner that as a whole would not otherwise exist in nature. DNAconstructs contain the information necessary to direct the expression ofpolypeptides of interest. DNA constructs can include promoters,enhancers and transcription terminators. DNA constructs containing theinformation necessary to direct the secretion of a polypeptide will alsocontain at least one secretory signal sequence.

Domain, as used herein, means a region of a polypeptide (includingproteins as that term is defined) having some distinctive physicalfeature or role including for example an independently folded structurecomposed of one section of a polypeptide chain. A domain may contain thesequence of the distinctive physical feature of the polypeptide or itmay contain a fragment of the physical feature which retains its bindingcharacteristics (i.e., it can bind to a second domain). A domain may beassociated with another domain. In other words, a first domain maynaturally bind to a second domain.

A fragment, as used herein, refers to a peptide or polypeptidecomprising an amino acid sequence of at least 2 contiguous amino acidresidues, of at least 5 contiguous amino acid residues, of at least 10contiguous amino acid residues, of at least 15 contiguous amino acidresidues, of at least 20 contiguous amino acid residues, of at least 25contiguous amino acid residues, of at least 40 contiguous amino acidresidues, of at least 50 contiguous amino acid residues, of at least 100contiguous amino acid residues, or of at least 200 contiguous amino acidresidues or any deletion or truncation of a protein, peptide, orpolypeptide.

Hemostasis, as used herein, means the stoppage of bleeding orhemorrhage; or the stoppage of blood flow through a blood vessel or bodypart.

Hemostatic disorder, as used herein, means a genetically inherited oracquired condition characterized by a tendency to hemorrhage, eitherspontaneously or as a result of trauma, due to an impaired ability orinability to form a fibrin clot.

Linked, as used herein, refers to a first nucleic acid sequencecovalently joined to a second nucleic acid sequence. The first nucleicacid sequence can be directly joined or juxtaposed to the second nucleicacid sequence or alternatively an intervening sequence can covalentlyjoin the first sequence to the second sequence. Linked as used hereincan also refer to a first amino acid sequence covalently, ornon-covalently, joined to a second amino acid sequence. The first aminoacid sequence can be directly joined or juxtaposed to the second aminoacid sequence or alternatively an intervening sequence can covalentlyjoin the first amino acid sequence to the second amino acid sequence.

Operatively linked, as used herein, means a first nucleic acid sequencelinked to a second nucleic acid sequence such that both sequences arecapable of being expressed as a biologically active protein or peptide.

Polypeptide, as used herein, refers to a polymer of amino acids and doesnot refer to a specific length of the product; thus, peptides,oligopeptides, and proteins are included within the definition ofpolypeptide. This term does not exclude post-expression modifications ofthe polypeptide, for example, glycosylation, acetylation,phosphorylation, pegylation, addition of a lipid moiety, or the additionof any organic or inorganic molecule. Included within the definition,are for example, polypeptides containing one or more analogs of an aminoacid (including, for example, unnatural amino acids) and polypeptideswith substituted linkages, as well as other modifications known in theart, both naturally occurring and non-naturally occurring.

High stringency, as used herein, includes conditions readily determinedby the skilled artisan based on, for example, the length of the DNA.Generally, such conditions are defined in Sambrook et al. MolecularCloning: A Laboratory Manual, 2 ed. Vol. 1, pp. 1.101-104, Cold SpringHarbor Laboratory Press (1989), and include use of a prewashing solutionfor the nitrocellulose filters 5×SSC, 0.5% SDS, 1.0 mM EDTA (PH 8.0),hybridization conditions of 50% formamide, 6×SSC at 42° C. (or othersimilar hybridization solution, such as Stark's solution, in 50%formamide at 42° C., and with washing at approximately 68° C., 0.2×SSC,0.1% SDS. The skilled artisan will recognize that the temperature andwash solution salt concentration can be adjusted as necessary accordingto factors such as the length of the probe.

Moderate stringency, as used herein, include conditions that can bereadily determined by those having ordinary skill in the art based on,for example, the length of the DNA. The basic conditions are set forthby Sambrook et al. Molecular Cloning: A Laboratory Manual, 2d ed. Vol.1, pp. 1.101-104, Cold Spring Harbor Laboratory Press (1989), andinclude use of a prewashing solution for the nitrocellulose filters5×SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0), hybridization conditions of 50%formamide, 6×SSC at 42° C. (or other similar hybridization solution,such as Stark's solution, in 50% formamide at 42° C.), and washingconditions of 60° C., 0.5×SSC, 0.1% SDS.

A small inorganic molecule, as used herein means a molecule containingno carbon atoms and being no larger than 50 kD.

A small organic molecule, as used herein means a molecule containing atleast one carbon atom and being no larger than 50 kD.

Treat, treatment, treating, as used herein means, any of the following:the reduction in severity of a disease or condition; the reduction inthe duration of a disease course; the amelioration of one or moresymptoms associated with a disease or condition; the provision ofbeneficial effects to a subject with a disease or condition, withoutnecessarily curing the disease or condition, the prophylaxis of one ormore symptoms associated with a disease or condition.

B. Improvements Offered by Certain Embodiments of the Invention

The invention provides for chimeric proteins (monomer-dimer hybrids)comprising a first and a second polypeptide chain, wherein said firstchain comprises a biologically active molecule and at least a portion ofan immunoglobulin constant region, and said second chain comprises atleast a portion of an immunoglobulin constant region without anybiologically active molecule or variable region of an immunoglobulin.FIG. 1 contrasts traditional fusion protein dimers with one example ofthe monomer-dimer hybrid of the invention. In this example, thebiologically active molecule is EPO and the portion of an immunoglobulinis IgG Fc region.

Like other chimeric proteins comprised of at least a portion of animmunoglobulin constant region, the invention provides for chimericproteins which afford enhanced stability and increased bioavailabilityof the chimeric protein compared to the biologically active moleculealone. Additionally, however, because only one of the two chainscomprises the biologically active molecule, the chimeric protein has alower molecular weight than a chimeric protein wherein all chainscomprise a biologically active molecule and while not wishing to bebound by any theory, this may result in the chimeric protein being morereadily transcytosed across the epithelium barrier, e.g., by binding tothe FcRn receptor thereby increasing the half-life of the chimericprotein. In one embodiment, the invention thus provides for an improvednon-invasive method (e.g. via any mucosal surface, such as, orally,buccally, sublingually, nasally, rectally, vaginally, or via pulmonaryor occular route) of administering a therapeutic chimeric protein of theinvention. The invention thus provides methods of attaining therapeuticlevels of the chimeric proteins of the invention using less frequent andlower doses compared to previously described chimeric proteins (e.g.chimeric proteins comprised of at least a portion of an immunoglobulinconstant region and a biologically active molecule, wherein all chainsof the chimeric protein comprise a biologically active molecule).

In another embodiment, the invention provides an invasive method, e.g.,subcutaneously, intravenously, of administering a therapeutic chimericprotein of the invention. Invasive administration of the therapeuticchimeric protein of the invention provides for an increased half life ofthe therapeutic chimeric protein which results in using less frequentand lower doses compared to previously described chimeric proteins (e.g.chimeric proteins comprised of at least a portion of an immunoglobulinconstant region and a biologically active molecule, wherein all chainsof the chimeric protein comprise a biologically active molecule).

Yet another advantage of a chimeric protein wherein only one of thechains comprises a biologically active molecule is the enhancedaccessibility of the biologically active molecule for its target cell ormolecule resulting from decreased steric hindrance, decreasedhydrophobic interactions, decreased ionic interactions, or decreasedmolecular weight compared to a chimeric protein wherein all chains arecomprised of a biologically active molecule.

C. Chimeric Proteins

The invention relates to chimeric proteins comprising one biologicallyactive molecule, at least a portion of an immunoglobulin constantregion, and optionally at least one linker The portion of animmunoglobulin will have both an N, or an amino terminus, and a C, orcarboxy terminus. The chimeric protein may have the biologically activemolecule linked to the N terminus of the portion of an immunoglobulin.Alternatively, the biologically active molecule may be linked to the Cterminus of the portion of an immunoglobulin. In one embodiment, thelinkage is a covalent bond. In another embodiment, the linkage is anon-covalent bond.

The chimeric protein can optionally comprise at least one linker; thus,the biologically active molecule does not have to be directly linked tothe portion of an immunoglobulin constant region. The linker canintervene in between the biologically active molecule and the portion ofan immunoglobulin constant region. The linker can be linked to the Nterminus of the portion of an immunoglobulin constant region, or the Cterminus of the portion of an immunoglobulin constant region. If thebiologically active molecule is comprised of at least one amino acid thebiologically active molecule will have an N terminus and a C terminusand the linker can be linked to the N terminus of the biologicallyactive molecule, or the C terminus the biologically active molecule.

The invention relates to a chimeric protein of the formula X-L_(a)-F:For F:F-L_(a)-X, wherein X is a biologically active molecule, L is anoptional linker, F is at least a portion of an immunoglobulin constantregion and, a is any integer or zero. The invention also relates to achimeric protein of the formula T_(a)-X-L_(a)-F:F or T_(a)-F:F-L_(a)-X,wherein X is a biologically active molecule, L is an optional linker, Fis at least a portion of an immunoglobulin constant region, a is anyinteger or zero, T is a second linker or alternatively a tag that can beused to facilitate purification of the chimeric protein, e.g., a FLAGtag, a histidine tag, a GST tag, a maltose binding protein tag and (:)represents a chemical association, e.g. at least one non-peptide bond.In certain embodiments, the chemical association, i.e., (:) is acovalent bond. In other embodiments, the chemical association, i.e., (:)is a non-covalent interaction, e.g., an ionic interaction, a hydrophobicinteraction, a hydrophilic interaction, a Van der Waals interaction, ahydrogen bond. It will be understood by the skilled artisan that when aequals zero X will be directly linked to F. Thus, for example, a may be0, 1, 2, 3, 4, 5, or more than 5.

In one embodiment, the chimeric protein of the invention comprises theamino acid sequence of FIG. 2 a (SEQ ID NO:6). In one embodiment, thechimeric protein of the invention comprises the amino acid sequence ofFIG. 2 b (SEQ ID NO:8). In one embodiment, the chimeric protein of theinvention comprises the amino acid sequence of FIG. 2 c (SEQ ID NO:10).In one embodiment, the chimeric protein of the invention comprises theamino acid sequence of FIG. 2 d (SEQ ID NO:12). In one embodiment, thechimeric protein of the invention comprises the amino acid sequence ofFIG. 2 e (SEQ ID NO:14). In one embodiment, the chimeric protein of theinvention comprises the amino acid sequence of FIG. 2 f (SEQ ID NO:16).In one embodiment, the chimeric protein of the invention comprises theamino acid sequence of FIG. 2 g (SEQ ID NO:18). In one embodiment, thechimeric protein of the invention comprises the amino acid sequence ofFIG. 2 h (SEQ ID NO:20). In one embodiment, the chimeric protein of theinvention comprises the amino acid sequence of FIG. 2 i (SEQ ID NO:22).In one embodiment, the chimeric protein of the invention comprises theamino acid sequence of FIG. 2 j (SEQ ID NO:24). In one embodiment, thechimeric protein of the invention comprises the amino acid sequence ofFIG. 17 b (SEQ ID NO: 99).

1. Chimeric Protein Variants

Derivatives of the chimeric proteins of the invention, antibodiesagainst the chimeric proteins of the invention and antibodies againstbinding partners of the chimeric proteins of the invention are allcontemplated, and can be made by altering their amino acids sequences bysubstitutions, additions, and/or deletions/truncations or by introducingchemical modification that result in functionally equivalent molecules.It will be understood by one of ordinary skill in the art that certainamino acids in a sequence of any protein may be substituted for otheramino acids without adversely affecting the activity of the protein.

Various changes may be made in the amino acid sequences of the chimericproteins of the invention or DNA sequences encoding therefore withoutappreciable loss of their biological activity, function, or utility.Derivatives, analogs, or mutants resulting from such changes and the useof such derivatives is within the scope of the present invention. In aspecific embodiment, the derivative is functionally active, i.e.,capable of exhibiting one or more activities associated with thechimeric proteins of the invention, e.g., FcRn binding, viralinhibition, hemostasis, production of red blood cells. Many assayscapable of testing the activity of a chimeric protein comprising abiologically active molecule are known in the art. Where thebiologically active molecule is an HIV inhibitor, activity can be testedby measuring reverse transcriptase activity using known methods (see,e.g., Barre-Sinoussi et al. 1983, Science 220:868; Gallo et al. 1984,Science 224:500). Alternatively, activity can be measured by measuringfusogenic activity (see, e.g., Nussbaum et al. 1994, J. Virol.68(9):5411). Where the biological activity is hemostasis, a StaCLotFVIIa-rTF assay can be performed to assess activity of Factor VIIaderivatives (Johannessen et al. 2000, Blood Coagulation and Fibrinolysis11:S159).

Substitutes for an amino acid within the sequence may be selected fromother members of the class to which the amino acid belongs (see Table1). Furthermore, various amino acids are commonly substituted withneutral amino acids, e.g., alanine, leucine, isoleucine, valine,proline, phenylalanine, tryptophan, and methionine (see, e.g., MacLennanet al. 1998, Acta Physiol. Scand. Suppl. 643:55-67; Sasaki et al. 1998,Adv. Biophys. 35:1-24).

TABLE 1 Original Exemplary Typical Residues Substitutions SubstitutionsAla (A) Val, Leu, Ile Val Arg (R) Lys, Gln, Asn Lys Asn (N) Gln Gln Asp(D) Glu Glu Cys (C) Ser, Ala Ser Gln (Q) Asn Asn Gly (G) Pro, Ala AlaHis (H) Asn, Gln, Lys, Arg Arg Ile (I) Leu, Val, Met, Ala, Leu Phe,Norleucine Leu (L) Norleucine, Ile, Val, Ile Met, Ala, Phe Lys (K) Arg,Arg 1,4-Diamino-butyric Acid, Gln, Asn Met (M) Leu, Phe, Ile Leu Phe (F)Leu, Val, Ile, Ala, Tyr Leu Pro (P) Ala Gly Ser (S) Thr, Ala, Cys ThrThr (T) Ser Ser Trp (W) Tyr, Phe Tyr Tyr (Y) Trp, Phe, Thr, Ser Phe Val(V) Ile, Met, Leu, Phe, Ala, Leu Norleucine

2. Biologically Active Molecules

The invention contemplates the use of any biologically active moleculeas the therapeutic molecule of the invention. The biologically activemolecule can be a polypeptide. The biologically active molecule can be asingle amino acid. The biologically active molecule can include amodified polypeptide.

The biologically active molecule can include a lipid molecule (e.g. asteroid or cholesterol, a fatty acid, a triacylglycerol,glycerophospholipid, or sphingolipid). The biologically active moleculecan include a sugar molecule (e.g. glucose, sucrose, mannose). Thebiologically active molecule can include a nucleic acid molecule (e.g.DNA, RNA). The biologically active molecule can include a small organicmolecule or a small inorganic molecule.

a. Cytokines and Growth Factors

In one embodiment, the biologically active molecule is a growth factor,hormone or cytokine or analog or fragment thereof. The biologicallyactive molecule can be any agent capable of inducing cell growth andproliferation. In a specific embodiment, the biologically activemolecule is any agent which can induce erythrocytes to proliferate.Thus, one example of a biologically active molecule contemplated by theinvention is EPO. The biologically active molecule can also include, butis not limited to, RANTES, MIP1α, MIP1β, IL-2, IL-3, GM-CSF, growthhormone, tumor necrosis factor (e.g. TNFα or β).

The biologically active molecule can include interferon α, whethersynthetically or recombinantly produced, including but not limited to,any one of the about twenty-five structurally related subtypes, as forexample interferon-α2a, now commercially available for clinical use(ROFERON®, Roche) and interferon-α2b also approved for clinical use(INTRONO, Schering) as well as genetically engineered versions ofvarious subtypes, including, but not limited to, commercially availableconsensus interferon α (INFERGEN®, Intermune, developed by Amgen) andconsensus human leukocyte interferon see, e.g., U.S. Pat. Nos.4,695,623; 4,897,471, interferon β, epidermal growth factor,gonadotropin releasing hormone (GnRH), leuprolide, follicle stimulatinghormone, progesterone, estrogen, or testosterone.

A list of cytokines and growth factors which may be used in the chimericprotein of the invention has been previously described (see, e.g., U.S.Pat. Nos. 6,086,875, 6,485,726, 6,030,613; WO 03/077834;US2003-0235536A1).

b. Antiviral Agents

In one embodiment, the biologically active molecule is an antiviralagent, including fragments and analogs thereof. An antiviral agent caninclude any molecule that inhibits or prevents viral replication, orinhibits or prevents viral entry into a cell, or inhibits or preventsviral egress from a cell. In one embodiment, the antiviral agent is afusion inhibitor. In one embodiment, the antiviral agent is a cytokinewhich inhibits viral replication. In another embodiment, the antiviralagent is interferon α.

The viral fusion inhibitor for use in the chimeric protein can be anymolecule which decreases or prevents viral penetration of a cellularmembrane of a target cell. The viral fusion inhibitor can be anymolecule that decreases or prevents the formation of syncytia between atleast two susceptible cells. The viral fusion inhibitor can be anymolecule that decreases or prevents the joining of a lipid bilayermembrane of a eukaryotic cell and a lipid bilayer of an enveloped virus.Examples of enveloped virus include, but are not limited to HIV-1,HIV-2, SIV, influenza, parainfluenza, Epstein-Barr virus, CMV, herpessimplex 1, herpes simplex 2 and respiratory syncytia virus.

The viral fusion inhibitor can be any molecule that decreases orprevents viral fusion including, but not limited to, a polypeptide, asmall organic molecule or a small inorganic molecule. In one embodiment,the fusion inhibitor is a polypeptide. In one embodiment, the viralfusion inhibitor is a polypeptide of 3-36 amino acids. In anotherembodiment, the viral fusion inhibitor is a polypeptide of 3-50 aminoacids, 10-65 amino acids, 10-75 amino acids. The polypeptide can becomprised of a naturally occurring amino acid sequence (e.g. a fragmentof gp41) including analogs and mutants thereof or the polypeptide can becomprised of an amino acid sequence not found in nature, so long as thepolypeptide exhibits viral fusion inhibitory activity.

In one embodiment, the viral fusion inhibitor is a polypeptide,identified as being a viral fusion inhibitor using at least one computeralgorithm, e.g., ALLMOTI5, 107×178×4 and PLZIP (see, e.g., U.S. Pat.Nos. 6,013,263; 6,015,881; 6,017,536; 6,020,459; 6,060,065; 6,068,973;6,093,799; and 6,228,983).

In one embodiment, the viral fusion inhibitor is an HIV fusioninhibitor. In one embodiment, HIV is HIV-1. In another embodiment, HIVis HIV-2. In one embodiment, the HIV fusion inhibitor is a polypeptidecomprised of a fragment of the gp41 envelope protein of HIV-1. The HIVfusion inhibitor can comprise, e.g., T20 (SEQ ID NO:1) or an analogthereof, T21 (SEQ ID NO:2) or an analog thereof, T1249 (SEQ ID NO:3) oran analog thereof, N_(CCG)gp41 (Louis et al. 2001, J. Biol. Chem.276:(31)29485) or an analog thereof, or 5 helix (Root et al. 2001,Science 291:884) or an analog thereof.

Assays known in the art can be used to test for viral fusion inhibitingactivity of a polypeptide, a small organic molecule, or a smallinorganic molecule. These assays include a reverse transcriptase assay,a p24 assay, or syncytia formation assay (see, e.g., U.S. Pat. No.5,464,933).

A list of antiviral agents which may be used in the chimeric protein ofthe invention has been previously described (see, e.g., U.S. Pat. Nos.6,086,875, 6,485,726, 6,030,613; WO 03/077834; US2003-0235536A1).

c. Hemostatic Agents

In one embodiment, the biologically active molecule is a clotting factoror other agent that promotes hemostasis, including fragments and analogsthereof. The clotting factor can include any molecule that has clottingactivity or activates a molecule with clotting activity. The clottingfactor can be comprised of a polypeptide. The clotting factor can be, asan example, but not limited to Factor VIII, Factor IX, Factor XI, FactorXII, fibrinogen, prothrombin, Factor V, Factor VII, Factor X, FactorXIII or von Willebrand Factor. In one embodiment, the clotting factor isFactor VII or Factor VIIa. The clotting factor can be a factor thatparticipates in the extrinsic pathway. The clotting factor can be afactor that participates in the intrinsic pathway. Alternatively, theclotting factor can be a factor that participates in both the extrinsicand intrinsic pathway.

The clotting factor can be a human clotting factor or a non-humanclotting factor, e.g., derived from a non-human primate, a pig or anymammal. The clotting factor can be chimeric clotting factor, e.g., theclotting factor can comprise a portion of a human clotting factor and aportion of a porcine clotting factor or a portion of a first non-humanclotting factor and a portion of a second non-human clotting factor.

The clotting factor can be an activated clotting factor. Alternatively,the clotting factor can be an inactive form of a clotting factor, e.g.,a zymogen. The inactive clotting factor can undergo activationsubsequent to being linked to at least a portion of an immunoglobulinconstant region. The inactive clotting factor can be activatedsubsequent to administration to a subject. Alternatively, the inactiveclotting factor can be activated prior to administration.

In certain embodiments an endopeptidase, e.g., paired basic amino acidcleaving enzyme (PACE), or any PACE family member, such as PCSK1-9,including truncated versions thereof, or its yeast equivalent Kex2 fromS. cerevisiae and truncated versions of Kex2 (Kex2 1-675) (see, e.g.,U.S. Pat. Nos. 5,077,204; 5,162,220; 5,234,830; 5,885,821; 6,329,176)may be used to cleave a propetide to form the mature chimeric protein ofthe invention (e.g. factor VII, factor IX).

d. Other Proteinaceous Biologically Active Molecules

In one embodiment, the biologically active molecule is a receptor or afragment or analog thereof. The receptor can be expressed on a cellsurface, or alternatively the receptor can be expressed on the interiorof the cell. The receptor can be a viral receptor, e.g., CD4, CCR5,CXCR4, CD21, CD46. The biologically active molecule can be a bacterialreceptor. The biologically active molecule can be an extra-cellularmatrix protein or fragment or analog thereof, important in bacterialcolonization and infection (see, e.g., U.S. Pat. Nos. 5,648,240;5,189,015; 5,175,096) or a bacterial surface protein important inadhesion and infection (see, e.g., U.S. Pat. No. 5,648,240). Thebiologically active molecule can be a growth factor, hormone or cytokinereceptor, or a fragment or analog thereof, e.g., TNFα receptor, theerythropoietin receptor, CD25, CD122, or CD132.

A list of other proteinaceous molecules which may be used in thechimeric protein of the invention has been previously described (see,e.g., U.S. Pat. Nos. 6,086,875; 6,485,726; 6,030,613; WO 03/077834;U52003-0235536A1).

e. Nucleic Acids

In one embodiment, the biologically active molecule is a nucleic acid,e.g., DNA, RNA. In one specific embodiment, the biologically activemolecule is a nucleic acid that can be used in RNA interference (RNAi).The nucleic acid molecule can be as an example, but not as a limitation,an anti-sense molecule or a ribozyme or an aptamer.

Antisense RNA and DNA molecules act to directly block the translation ofmRNA by hybridizing to targeted mRNA and preventing protein translation.Antisense approaches involve the design of oligonucleotides that arecomplementary to a target gene mRNA. The antisense oligonucleotides willbind to the complementary target gene mRNA transcripts and preventtranslation. Absolute complementarily, is not required.

A sequence “complementary” to a portion of an RNA, as referred toherein, means a sequence having sufficient complementarity to be able tohybridize with the RNA, forming a stable duplex; in the case ofdouble-stranded antisense nucleic acids, a single strand of the duplexDNA may thus be tested, or triplex formation may be assayed. The abilityto hybridize will depend on both the degree of complementarity and thelength of the antisense nucleic acid. Generally, the longer thehybridizing nucleic acid, the more base mismatches with an RNA it maycontain and still form a stable duplex (or triplex, as the case may be).One skilled in the art can ascertain a tolerable degree of mismatch byuse of standard procedures to determine the melting point of thehybridized complex.

Antisense nucleic acids should be at least six nucleotides in length,and are preferably oligonucleotides ranging from 6 to about 50nucleotides in length. In specific aspects, the oligonucleotide is atleast 10 nucleotides, at least 17 nucleotides, at least 25 nucleotidesor at least 50 nucleotides.

The oligonucleotides can be DNA or RNA or chimeric mixtures orderivatives or modified versions thereof, single-stranded ordouble-stranded. The oligonucleotide can be modified at the base moiety,sugar moiety, or phosphate backbone, for example, to improve stabilityof the molecule, hybridization, etc. The oligonucleotide may includeother appended groups such as polypeptides (e.g. for targeting host cellreceptors in vivo), or agents facilitating transport across the cellmembrane (see, e.g., Letsinger et al. 1989, Proc. Natl. Acad. Sci. USA86:6553; Lemaitre et al. 1987, Proc. Natl. Acad. Sci. USA 84:648; WO88/09810,) or the blood-brain barrier (see, e.g., WO 89/10134),hybridization-triggered cleavage agents (see, e.g., Krol et al. 1988,BioTechniques 6:958) or intercalating agents (see, e.g., Zon 1988,Pharm. Res. 5:539). To this end, the oligonucleotide may be conjugatedto another molecule, e.g., a polypeptide, hybridization triggeredcross-linking agent, transport agent, or hybridization-triggeredcleavage agent.

Ribozyme molecules designed to catalytically cleave target gene mRNAtranscripts can also be used to prevent translation of target gene mRNAand, therefore, expression of target gene product. (See, e.g., WO90/11364; Sarver et al. 1990, Science 247, 1222-1225).

Ribozymes are enzymatic RNA molecules capable of catalyzing the specificcleavage of RNA. (See Rossi 1994, Current Biology 4:469). The mechanismof ribozyme action involves sequence specific hybridization of theribozyme molecule to complementary target RNA, followed by anendonucleolytic cleavage event. The composition of ribozyme moleculesmust include one or more sequences complementary to the target genemRNA, and must include the well known catalytic sequence responsible formRNA cleavage. For this sequence, see, e.g., U.S. Pat. No. 5,093,246.

In one embodiment, ribozymes that cleave mRNA at site specificrecognition sequences can be used to destroy target gene mRNAs. Inanother embodiment, the use of hammerhead ribozymes is contemplated.Hammerhead ribozymes cleave mRNAs at locations dictated by flankingregions that form complementary base pairs with the target mRNA. Thesole requirement is that the target mRNA have the following sequence oftwo bases: 5′-UG-3′. The construction and production of hammerheadribozymes is well known in the art and is described more fully in Myers1995, Molecular Biology and Biotechnology: A Comprehensive DeskReference, VCH Publishers, New York, and in Haseloff and Gerlach 1988,Nature, 334:585.

f. Small Molecules

The invention also contemplates the use of any therapeutic smallmolecule or drug as the biologically active molecule in the chimericprotein of the invention. A list of small molecules and drugs which maybe used in the chimeric protein of the invention has been previouslydescribed (see, e.g., U.S. Pat. Nos. 6,086,875; 6,485,726; 6,030,613; WO03/077834; US2003-0235536A1).

2. Immunoglobulins

The chimeric proteins of the invention comprise at least a portion of animmunoglobulin constant region. Immunoglobulins are comprised of fourprotein chains that associate covalently-two heavy chains and two lightchains. Each chain is further comprised of one variable region and oneconstant region. Depending upon the immunoglobulin isotype, the heavychain constant region is comprised of 3 or 4 constant region domains(e.g. CH1, CH2, CH3, CH4). Some isotypes are further comprised of ahinge region.

The portion of an immunoglobulin constant region can be obtained fromany mammal. The portion of an immunoglobulin constant region can includea portion of a human immunoglobulin constant region, a non-human primateimmunoglobulin constant region, a bovine immunoglobulin constant region,a porcine immunoglobulin constant region, a murine immunoglobulinconstant region, an ovine immunoglobulin constant region or a ratimmunoglobulin constant region.

The portion of an immunoglobulin constant region can be producedrecombinantly or synthetically. The immunoglobulin can be isolated froma cDNA library. The portion of an immunoglobulin constant region can beisolated from a phage library (See, e.g., McCafferty et al. 1990, Nature348:552, Kang et al. 1991, Proc. Natl. Acad. Sci. USA 88:4363; EP 0 589877 B1). The portion of an immunoglobulin constant region can beobtained by gene shuffling of known sequences (Mark et al. 1992,Bio/Technol. 10:779). The portion of an immunoglobulin constant regioncan be isolated by in vivo recombination (Waterhouse et al. 1993, Nucl.Acid Res. 21:2265). The immunoglobulin can be a humanized immunoglobulin(U.S. Pat. No. 5,585,089, Jones et al. 1986, Nature 332:323).

The portion of an immunoglobulin constant region can include a portionof an IgG, an IgA, an IgM, an IgD, or an IgE. In one embodiment, theimmunoglobulin is an IgG. In another embodiment, the immunoglobulin isIgG1. In another embodiment, the immunoglobulin is IgG2.

The portion of an immunoglobulin constant region can include the entireheavy chain constant region, or a fragment or analog thereof. In oneembodiment, a heavy chain constant region can comprise a CH1 domain, aCH2 domain, a CH3 domain, and/or a hinge region. In another embodiment,a heavy chain constant region can comprise a CH1 domain, a CH2 domain, aCH3 domain, and/or a CH4 domain.

The portion of an immunoglobulin constant region can include an Fcfragment. An Fc fragment can be comprised of the CH2 and CH3 domains ofan immunoglobulin and the hinge region of the immunoglobulin. The Fcfragment can be the Fc fragment of an IgG1, an IgG2, an IgG3 or an IgG4.In one specific embodiment, the portion of an immunoglobulin constantregion is an Fc fragment of an IgG1. In another embodiment, the portionof an immunoglobulin constant region is an Fc fragment of an IgG2.

In another embodiment, the portion of an immunoglobulin constant regionis an Fc neonatal receptor (FcRn) binding partner. An FcRn bindingpartner is any molecule that can be specifically bound by the FcRnreceptor with consequent active transport by the FcRn receptor of theFcRn binding partner. Specifically bound refers to two molecules forminga complex that is relatively stable under physiologic conditions.Specific binding is characterized by a high affinity and a low tomoderate capacity as distinguished from nonspecific binding whichusually has a low affinity with a moderate to high capacity. Typically,binding is considered specific when the affinity constant K_(A) ishigher than 10⁶ M⁻¹, or more preferably higher than 10⁸ M⁻¹. Ifnecessary, non-specific binding can be reduced without substantiallyaffecting specific binding by varying the binding conditions. Theappropriate binding conditions such as concentration of the molecules,ionic strength of the solution, temperature, time allowed for binding,concentration of a blocking agent (e.g. serum albumin, milk casein),etc., may be optimized by a skilled artisan using routine techniques.

The FcRn receptor has been isolated from several mammalian speciesincluding humans. The sequences of the human FcRn, monkey FcRn rat FcRn,and mouse FcRn are known (Story et al. 1994, J. Exp. Med. 180:2377). TheFcRn receptor binds IgG (but not other immunoglobulin classes such asIgA, IgM, IgD, and IgE) at relatively low pH, actively transports theIgG transcellularly in a luminal to serosal direction, and then releasesthe IgG at relatively higher pH found in the interstitial fluids. It isexpressed in adult epithelial tissue (U.S. Pat. Nos. 6,485,726,6,030,613, 6,086,875; WO 03/077834; US2003-0235536A1) including lung andintestinal epithelium (Israel et al. 1997, Immunology 92:69) renalproximal tubular epithelium (Kobayashi et al. 2002, Am. J. Physiol.Renal Physiol. 282:F358) as well as nasal epithelium, vaginal surfaces,and biliary tree surfaces.

FcRn binding partners of the present invention encompass any moleculethat can be specifically bound by the FcRn receptor including whole IgG,the Fc fragment of IgG, and other fragments that include the completebinding region of the FcRn receptor. The region of the Fc portion of IgGthat binds to the FcRn receptor has been described based on X-raycrystallography (Burmeister et al. 1994, Nature 372:379). The majorcontact area of the Fc with the FcRn is near the junction of the CH2 andCH3 domains. Fc-FcRn contacts are all within a single Ig heavy chain.The FcRn binding partners include whole IgG, the Fc fragment of IgG, andother fragments of IgG that include the complete binding region of FcRn.The major contact sites include amino acid residues 248, 250-257, 272,285, 288, 290-291, 308-311, and 314 of the CH2 domain and amino acidresidues 385-387, 428, and 433-436 of the CH3 domain. References made toamino acid numbering of immunoglobulins or immunoglobulin fragments, orregions, are all based on Kabat et al. 1991, Sequences of Proteins ofImmunological Interest, U.S. Department of Public Health, Bethesda, Md.

The Fc region of IgG can be modified according to well recognizedprocedures such as site directed mutagenesis and the like to yieldmodified IgG or Fc fragments or portions thereof that will be bound byFcRn. Such modifications include modifications remote from the FcRncontact sites as well as modifications within the contact sites thatpreserve or even enhance binding to the FcRn. For example, the followingsingle amino acid residues in human IgG1 Fc (Fcγ1) can be substitutedwithout significant loss of Fc binding affinity for FcRn: P238A, S239A,K246A, K248A, D249A, M252A, T256A, E258A, T260A, D265A, S267A, H268A,E269A, D270A, E272A, L274A, N276A, Y278A, D280A, V282A, E283A, H285A,N286A, T289A, K290A, R292A, E293A, E294A, Q295A, Y296F, N297A, S298A,Y300F, R301A, V303A, V305A, T307A, L309A, Q311A, D312A, N315A, K317A,E318A, K320A, K322A, S324A, K326A, A327Q, P329A, A330Q, P331A, E333A,K334A, T335A, S337A, K338A, K340A, Q342A, R344A, E345A, Q347A, R355A,E356A, M358A, T359A, K360A, N361A, Q362A, Y373A, S375A, D376A, A378Q,E380A, E382A, S383A, N384A, Q386A, E388A, N389A, N390A, Y391F, K392A,L398A, S400A, D401A, D413A, K414A, R416A, Q418A, 0419A, N421A, V422A,S424A, E430A, N434A, T437A, Q438A, K439A, S440A, S444A, and K447A, wherefor example P238A represents wildtype proline substituted by alanine atposition number 238. As an example, one specifc embodiment, incorporatesthe N297A mutation, removing a highly conserved N-glycosylation site. Inaddition to alanine other amino acids may be substituted for thewildtype amino acids at the positions specified above. Mutations may beintroduced singly into Fc giving rise to more than one hundred FcRnbinding partners distinct from native Fc. Additionally, combinations oftwo, three, or more of these individual mutations may be introducedtogether, giving rise to hundreds more FcRn binding partners. Moreover,one of the FcRn binding partners of the monomer-dimer hybrid may bemutated and the other FcRn binding partner not mutated at all, or theyboth may be mutated but with different mutations. Any of the mutationsdescribed herein, including N297A, may be used to modify Fc, regardlessof the biologically active molecule (e.g., EPO, IFN, Factor IX, T20).

Certain of the above mutations may confer new functionality upon theFcRn binding partner. For example, one embodiment incorporates N297A,removing a highly conserved N-glycosylation site. The effect of thismutation is to reduce immunogenicity, thereby enhancing circulating halflife of the FcRn binding partner, and to render the FcRn binding partnerincapable of binding to FcγRI, FcγRIIA, FcγRIIB, and FcγRIIIA, withoutcompromising affinity for FcRn (Routledge et al. 1995, Transplantation60:847; Friend et al. 1999, Transplantation 68:1632; Shields et al.1995, J. Biol. Chem. 276:6591). As a further example of newfunctionality arising from mutations described above affinity for FcRnmay be increased beyond that of wild type in some instances. Thisincreased affinity may reflect an increased “on” rate, a decreased “off”rate or both an increased “on” rate and a decreased “off” rate.Mutations believed to impart an increased affinity for FcRn includeT256A, T307A, E380A, and N434A (Shields et al. 2001, J. Biol. Chem.276:6591).

Additionally, at least three human Fc gamma receptors appear torecognize a binding site on IgG within the lower hinge region, generallyamino acids 234-237. Therefore, another example of new functionality andpotential decreased immunogenicity may arise from mutations of thisregion, as for example by replacing amino acids 233-236 of human IgG1“ELLG” (SEQ ID NO: 84) to the corresponding sequence from IgG2 “PVA”(with one amino acid deletion). It has been shown that FcγRI, FcγRII,and FcγRIII, which mediate various effector functions will not bind toIgG1 when such mutations have been introduced. Ward and Ghetie 1995,Therapeutic Immunology 2:77 and Armour et al. 1999, Eur. J. Immunol.29:2613.

In one embodiment, the FcRn binding partner is a polypeptide includingthe sequence PKNSSMISNTP (SEQ ID NO:26) and optionally further includinga sequence selected from HQSLGTQ (SEQ ID NO:27), HQNLSDGK (SEQ IDNO:28), HQNISDGK (SEQ ID NO:29), or VISSHLGQ (SEQ ID NO:30) (U.S. Pat.No. 5,739,277).

Two FcRn receptors can bind a single Fc molecule. Crystallographic datasuggest that each FcRn molecule binds a single polypeptide of the Fchomodimer. In one embodiment, linking the FcRn binding partner, e.g., anFc fragment of an IgG, to a biologically active molecule provides ameans of delivering the biologically active molecule orally, buccally,sublingually, rectally, vaginally, as an aerosol administered nasally orvia a pulmonary route, or via an ocular mute. In another embodiment, thechimeric protein can be administered invasively, e.g., subcutaneously,intravenously.

The skilled artisan will understand that portions of an immunoglobulinconstant region for use in the chimeric protein of the invention caninclude mutants or analogs thereof, or can include chemically modifiedimmunoglobulin constant regions (e.g. pegylated), or fragments thereof(see, e.g., Aslam and Dent 1998, Bioconjugation: Protein CouplingTechniques For the Biomedical Sciences Macmilan Reference, London). Inone instance, a mutant can provide for enhanced binding of an FcRnbinding partner for the FcRn. Also contemplated for use in the chimericprotein of the invention are peptide mimetics of at least a portion ofan immunoglobulin constant region, e.g., a peptide mimetic of an Fcfragment or a peptide mimetic of an FcRn binding partner. In oneembodiment, the peptide mimetic is identified using phage display or viachemical library screening (see, e.g., McCafferty et al. 1990, Nature348:552, Kang et al. 1991, Proc. Natl. Acad. Sci. USA 88:4363; EP 0 589877 B1).

3. Optional Linkers

The chimeric protein of the invention can optionally comprise at leastone linker molecule. The linker can be comprised of any organicmolecule. In one embodiment, the linker is polyethylene glycol (PEG). Inanother embodiment, the linker is comprised of amino acids. The linkercan comprise 1-5 amino acids, 1-10 amino acids, 1-20 amino acids, 10-50amino acids, 50-100 amino acids, 100-200 amino acids. In one embodiment,the linker is the eight amino acid linker EFAGAAAV (SEQ ID NO:31). Anyof the linkers described herein may be used in the chimeric protein ofthe invention, e.g., a monomer-dimer hybrid, including EFAGAAAV (SEQ IDNO: 31), regardless of the biologically active molecule (e.g. EPO, IFN,Factor IX).

The linker can comprise the sequence G_(n) (SEQ ID NO: 85). The linkercan comprise the sequence (GA)_(n) (SEQ ID NO:32). The linker cancomprise the sequence (GGS)_(n) (SEQ ID NO:33). The linker can comprisethe sequence (GGS)_(n) (GGGGS)_(n) (SEQ ID NO:34). In these instances, nmay be an integer from 1-10, i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10.Examples of linkers include, but are not limited to, GGG (SEQ ID NO:35),SGGSGGS (SEQ ID NO:36), GGSGGSGGSGGSGGG (SEQ ID NO:37), GGSGGSGGGGSGGGGS(SEQ ID NO:38), GGSGGSGGSGGSGGSGGS (SEQ ID NO:39). The linker does noteliminate or diminish the biological activity of the chimeric protein.Optionally, the linker enhances the biological activity of the chimericprotein, e.g., by further diminishing the effects of steric hindranceand making the biologically active molecule more accessible to itstarget binding site.

In one specific embodiment, the linker for interferon α is 15-25 aminoacids long. In another specific embodiment, the linker for interferon αis 15-20 amino acids long. In another specific embodiment, the linkerfor interferon α is 10-25 amino acids long. In another specificembodiment, the linker for interferon α is 15 amino acids long. In oneembodiment, the linker for interferon α is (GGGGS)_(n) (SEQ ID NO:40)where G represents glycine, S represents serine and n is an integer from1-10. In a specific embodiment, n is 3 (SEQ ID NO: 60).

The linker may also incorporate a moiety capable of being cleaved eitherchemically (e.g. hydrolysis of an ester bond), enzymatically (i.e.incorporation of a protease cleavage sequence) or photolytically (e.g.,a chromophore such as 3-amino-3-(2-nitrophenyl) proprionic acid (ANP))in order to release the biologically active molecule from the Fcprotein.

4. Chimeric Protein Dimerization Using Specific Binding Partners

In one embodiment, the chimeric protein of the invention comprises afirst polypeptide chain comprising at least a first domain, said firstdomain having at least one specific binding partner, and a secondpolypeptide chain comprising at least a second domain, wherein saidsecond domain, is a specific binding partner of said first domain. Thechimeric protein thus comprises a polypeptide capable of dimerizing withanother polypeptide due to the interaction of the first domain and thesecond domain. Methods of dimerizing antibodies using heterologousdomains are known in the art (U.S. Pat. Nos. 5,807,706 and 5,910,573;Kostelny et al. 1992, J. Immunol. 148(5):1547).

Dimerization can occur by formation of a covalent bond, or alternativelya non-covalent bond, e.g., hydrophobic interaction, Van der Waal'sforces, interdigitation of amphiphilic peptides such as, but not limitedto, alpha helices, charge-charge interactions of amino acids bearingopposite charges, such as, but not limited to, lysine and aspartic acid,arginine and glutamic acid. In one embodiment, the domain is a helixbundle comprising a helix, a turn and another helix. In anotherembodiment, the domain is a leucine zipper comprising a peptide havingseveral repeating amino acids in which every seventh amino acid is aleucine residue. In one embodiment, the specific binding partners arefos/jun. (see Branden et al. 1991, Introduction To Protein Structure,Garland Publishing, New York).

In another embodiment, binding is mediated by a chemical linkage (see,e.g., Brennan et al. 1985, Science 229:81). In this embodiment, intactimmunoglobulins, or chimeric proteins comprised of at least a portion ofan immunoglobulin constant region are cleaved to generate heavy chainfragments. These fragments are reduced in the presence of the dithiolcomplexing agent sodium arsenite to stabilize vicinal dithiols andprevent intermolecular disulfide formation. The fragments generated arethen converted to thionitrobenzoate (TNB) derivatives. One of the TNBderivatives is then reconverted to the heavy chain fragment thiol byreduction with mercaptoethylamine and is then mixed with an equimolaramount of the other TNB derivative to form a chimeric dimer.

D. Nucleic Acids

The invention relates to a first nucleic acid construct and a secondnucleic acid construct each comprising a nucleic acid sequence encodingat least a portion of the chimeric protein of the invention. In oneembodiment, the first nucleic acid construct comprises a nucleic acidsequence encoding a portion of an immunoglobulin constant regionoperatively linked to a second DNA sequence encoding a biologicallyactive molecule, and said second DNA construct comprises a DNA sequenceencoding an immunoglobulin constant region without the second DNAsequence encoding a biologically active molecule.

The biologically active molecule can include, for example, but not as alimitation, a viral fusion inhibitor, a clotting factor, a growth factoror hormone, or a receptor, or analog, or fragment of any of thepreceding. The nucleic acid sequences can also include additionalsequences or elements known in the art (e.g., promoters, enhancers, polyA sequences, affinity tags). In one embodiment, the nucleic acidsequence of the second construct can optionally include a nucleic acidsequence encoding a linker placed between the nucleic acid sequenceencoding the biologically active molecule and the portion of theimmunoglobulin constant region. The nucleic acid sequence of the secondDNA construct can optionally include a linker sequence placed before orafter the nucleic acid sequence encoding the biologically activemolecule and/or the portion of the immunoglobulin constant region.

In one embodiment, the nucleic acid construct is comprised of DNA. Inanother embodiment, the nucleic acid construct is comprised of RNA. Thenucleic acid construct can be a vector, e.g., a viral vector or aplasmid. Examples of viral vectors include, but are not limited to adenovirus vector, an adeno associated virus vector or a murine leukemiavirus vector. Examples of plasmids include but are not limited to pUC,pGEM and pGEX.

In one embodiment, the nucleic acid construct comprises the nucleic acidsequence of FIG. 3 a (SEQ ID NO:7). In one embodiment, the nucleic acidconstruct comprises the nucleic acid sequence of FIG. 3 b (SEQ ID NO:9).In one embodiment, the nucleic acid construct comprises the nucleic acidsequence of FIG. 3 c (SEQ ID NO:11). In one embodiment, the nucleic acidconstruct comprises the nucleic acid sequence of FIG. 3 d (SEQ IDNO:13). In one embodiment, the nucleic acid construct comprises thenucleic acid sequence of FIG. 3 e (SEQ ID NO:15). In one embodiment, thenucleic acid construct comprises the nucleic acid sequence of FIG. 3 f(SEQ ID NO:17). In one embodiment, the nucleic acid construct comprisesthe nucleic acid sequence of FIG. 3 g (SEQ ID NO:19). In one embodiment,the nucleic acid construct comprises the nucleic acid sequence of FIG. 3h (SEQ ID NO:21). In one embodiment, the nucleic acid constructcomprises the nucleic acid sequence of FIG. 3 i (SEQ ID NO:23). In oneembodiment, the nucleic acid construct comprises the nucleic acidsequence of FIG. 3 j (SEQ ID NO:25). In one embodiment, the nucleic acidconstruct comprises the nucleic acid sequence of FIG. 17 a (SEQ ID NO:98).

Due to the known degeneracy of the genetic code, wherein more than onecodon can encode the same amino acid, a DNA sequence can vary from thatshown in SEQ ID NOS:7, 9, 11, 13, 15, 17, 19, 21, 23, 25 or 98 and stillencode a polypeptide having the corresponding amino acid sequence of SEQID NOS:6, 8, 10, 12, 14, 16, 18, 20, 22, 24 or 99 respectively. Suchvariant DNA sequences can result from silent mutations (e.g. occurringduring PCR amplification), or can be the product of deliberatemutagenesis of a native sequence. The invention thus provides isolatedDNA sequences encoding polypeptides of the invention, chosen from: (a)DNA comprising the nucleotide sequence of SEQ ID NOS:7, 9, 11, 13, 15,17, 19, 21, 23, or 98; (b) DNA encoding the polypeptides of SEQ IDNOS:6, 8, 10, 12, 14, 16, 18, 20, 22, 24 or 99; (c) DNA capable ofhybridization to a DNA of (a) or (b) under conditions of moderatestringency and which encodes polypeptides of the invention; (d) DNAcapable of hybridization to a DNA of (a) or (b) under conditions of highstringency and which encodes polypeptides of the invention, and (e) DNAwhich is degenerate as a result of the genetic code to a DNA defined in(a), (b), (c), or (d) and which encode polypeptides of the invention. Ofcourse, polypeptides encoded by such DNA sequences are encompassed bythe invention.

In another embodiment, the nucleic acid molecules comprising a sequenceencoding the chimeric protein of the invention can also comprisenucleotide sequences that are at least 80% identical to a nativesequence. Also contemplated are embodiments in which a nucleic acidmolecules comprising a sequence encoding the chimeric protein of theinvention comprises a sequence that is at least 90% identical, at least95% identical, at least 98% identical, at least 99% identical, or atleast 99.9% identical to a native sequence. A native sequence caninclude any DNA sequence not altered by the human hand. The percentidentity may be determined by visual inspection and mathematicalcalculation. Alternatively, the percent identity of two nucleic acidsequences can be determined by comparing sequence information using theGAP computer program, version 6.0 described by Devereux et al. 1984,Nucl. Acids Res. 12:387, and available from the University of WisconsinGenetics Computer Group (UWGCG). The preferred default parameters forthe GAP program include: (1) a unary comparison matrix (containing avalue of 1 for identities and 0 for non identities) for nucleotides, andthe weighted comparison matrix of Gribskov and Burgess 1986, Nucl. AcidsRes. 14:6745, as described by Schwartz and Dayhoff, eds. 1979, Atlas ofProtein Sequence and Structure, National Biomedical Research Foundation,pp. 353-358; (2) a penalty of 3.0 for each gap and an additional 0.10penalty for each symbol in each gap; and (3) no penalty for end gaps.Other programs used by one skilled in the art of sequence comparison mayalso be used.

E. Synthesis of Chimeric Proteins

Chimeric proteins comprising at least a portion of an immunoglobulinconstant region and a biologically active molecule can be synthesizedusing techniques well known in the art. For example, the chimericproteins of the invention can be synthesized recombinantly in cells(see, e.g., Sambrook et al. 1989, Molecular Cloning A Laboratory Manual,Cold Spring Harbor Laboratory, N.Y. and Ausubel et al. 1989, CurrentProtocols in Molecular Biology, Greene Publishing Associates and WileyInterscience, N.Y.). Alternatively, the chimeric proteins of theinvention can be synthesized using known synthetic methods such as solidphase synthesis. Synthetic techniques are well known in the art (see,e.g., Merrifield, 1973, Chemical Polypeptides, (Katsoyannis andPanayotis eds.) pp. 335-61; Merrifield 1963, J. Am. Chem. Soc. 85:2149;Davis et al. 1985, Biochem. Intl. 10:394; Finn et al. 1976, The Proteins(3d ed.) 2:105; Erikson et al. 1976, The Proteins (3d ed.) 2:257; U.S.Pat. No. 3,941,763. Alternatively, the chimeric proteins of theinvention can be synthesized using a combination of recombinant andsynthetic methods. In certain applications, it may be beneficial to useeither a recombinant method or a combination of recombinant andsynthetic methods.

Nucleic acids encoding a biologically active molecule can be readilysynthesized using recombinant techniques well known in the art.Alternatively, the peptides themselves can be chemically synthesized.Nucleic acids of the invention may be synthesized by standard methodsknown in the art, e.g., by use of an automated DNA synthesizer (such asare commercially available from Biosearch, Applied Biosystems, etc.). Asexamples, phosphorothioate oligonucleotides may be synthesized by themethod of Stein et al. 1988, Nucl. Acids Res. 16:3209, methylphosphonateoligonucleotides can be prepared by use of controlled pore glass polymersupports as described in Sarin et al. 1988, Proc. Natl. Acad. Sci. USA85:7448. Additional methods of nucleic acid synthesis are known in theart. (see, e.g., U.S. Pat. Nos. 6,015,881; 6,281,331; 6,469,136).

DNA sequences encoding immunoglobulin constant regions, or fragmentsthereof, may be cloned from a variety of genomic or cDNA libraries knownin the art. The techniques for isolating such DNA sequences usingprobe-based methods are conventional techniques and are well known tothose skilled in the art. Probes for isolating such DNA sequences may bebased on published DNA sequences (see, for example, Hieter et al. 1980,Cell 22:197-207). The polymerase chain reaction (PCR) method disclosedby Mullis et al. (U.S. Pat. No. 4,683,195) and Mullis (U.S. Pat. No.4,683,202) may be used. The choice of library and selection of probesfor the isolation of such DNA sequences is within the level of ordinaryskill in the art. Alternatively, DNA sequences encoding immunoglobulinsor fragments thereof can be obtained from vectors known in the art tocontain immunoglobulins or fragments thereof.

For recombinant production, a first polynucleotide sequence encoding aportion of the chimeric protein of the invention (e.g. a portion of animmunoglobulin constant region) and a second polynucleotide sequenceencoding a portion of the chimeric protein of the invention (e.g. aportion of an immunoglobulin constant region and a biologically activemolecule) are inserted into appropriate expression vehicles, i.e.vectors which contains the necessary elements for the transcription andtranslation of the inserted coding sequence, or in the case of an RNAviral vector, the necessary elements for replication and translation.The nucleic acids encoding the chimeric protein are inserted into thevector in proper reading frame.

The expression vehicles are then transfected or co-transfected into asuitable target cell, which will express the polypeptides. Transfectiontechniques known in the art include, but are not limited to, calciumphosphate precipitation (Wigler et al. 1978, Cell 14:725) andelectroporation (Neumann et al. 1982, EMBO, J. 1:841), and liposomebased reagents. A variety of host-expression vector systems may beutilized to express the chimeric proteins described herein includingboth prokaryotic or eukaryotic cells. These include, but are not limitedto, microorganisms such as bacteria (e.g. E. coli) transformed withrecombinant bacteriophage DNA or plasmid DNA expression vectorscontaining an appropriate coding sequence; yeast or filamentous fungitransformed with recombinant yeast or fungi expression vectorscontaining an appropriate coding sequence; insect cell systems infectedwith recombinant virus expression vectors (e.g. baculovirus) containingan appropriate coding sequence; plant cell systems infected withrecombinant virus expression vectors (e.g. cauliflower mosaic virus ortobacco mosaic virus) or transformed with recombinant plasmid expressionvectors (e.g. Ti plasmid) containing an appropriate coding sequence; oranimal cell systems, including mammalian cells (e.g. CHO, Cos, HeLacells).

When the chimeric protein of the invention is recombinantly synthesizedin a prokaryotic cell it may be desirable to refold the chimericprotein. The chimeric protein produced by this method can be refolded toa biologically active conformation using conditions known in the art,e.g., denaturing under reducing conditions and then dialyzed slowly intoPBS.

Depending on the expression system used, the expressed chimeric proteinis then isolated by procedures well-established in the art (e.g.affinity chromatography, size exclusion chromatography, ion exchangechromatography).

The expression vectors can encode for tags that permit for easypurification of the recombinantly produced chimeric protein. Examplesinclude, but are not limited to vector pUR278 (Ruther et al. 1983, EMBOJ. 2:1791) in which the chimeric protein described herein codingsequences may be ligated into the vector in frame with the lac z codingregion so that a hybrid protein is produced; pGEX vectors may be used toexpress chimeric proteins of the invention with a glutathioneS-transferase (GST) tag. These proteins are usually soluble and caneasily be purified from cells by adsorption to glutathione-agarose beadsfollowed by elution in the presence of free glutathione. The vectorsinclude cleavage sites (thrombin or Factor Xa protease or PreScissionProtease™ (Pharmacia, Peapack, N.J.)) for easy removal of the tag afterpurification.

To increase efficiency of production, the polynucleotides can bedesigned to encode multiple units of the chimeric protein of theinvention separated by enzymatic cleavage sites. The resultingpolypeptide can be cleaved (e.g. by treatment with the appropriateenzyme) in order to recover the polypeptide units. This can increase theyield of polypeptides driven by a single promoter. When used inappropriate viral expression systems, the translation of eachpolypeptide encoded by the mRNA is directed internally in thetranscript; e.g., by an internal ribosome entry site, IRES. Thus, thepolycistronic construct directs the transcription of a single, largepolycistronic mRNA which, in turn, directs the translation of multiple,individual polypeptides. This approach eliminates the production andenzymatic processing of polyproteins and may significantly increaseyield of polypeptide driven by a single promoter.

Vectors used in transformation will usually contain a selectable markerused to identify transformants. In bacterial systems, this can includean antibiotic resistance gene such as ampicillin or kanamycin.Selectable markers for use in cultured mammalian cells include genesthat confer resistance to drugs, such as neomycin, hygromycin, andmethotrexate. The selectable marker may be an amplifiable selectablemarker. One amplifiable selectable marker is the DHFR gene. Anotheramplifiable marker is the DHFR cDNA (Simonsen and Levinson 1983, Proc.Natl. Acad. Sci. USA 80:2495). Selectable markers are reviewed by Thilly(Mammalian Cell Technology, Butterworth Publishers, Stoneham, Mass.) andthe choice of selectable markers is well within the level of ordinaryskill in the art.

Selectable markers may be introduced into the cell on a separate plasmidat the same time as the gene of interest, or they may be introduced onthe same plasmid. If on the same plasmid, the selectable marker and thegene of interest may be under the control of different promoters or thesame promoter, the latter arrangement producing a dicistronic message.Constructs of this type are known in the art (for example, U.S. Pat. No.4,713,339).

The expression elements of the expression systems vary in their strengthand specificities. Depending on the host/vector system utilized, any ofa number of suitable transcription and translation elements, includingconstitutive and inducible promoters, may be used in the expressionvector. For example, when cloning in bacterial systems, induciblepromoters such as pL of bacteriophage λ, plac, ptrp, ptac (ptrp-lachybrid promoter) and the like may be used; when cloning in insect cellsystems, promoters such as the baculovirus polyhedron promoter may beused; when cloning in plant cell systems, promoters derived from thegenome of plant cells (e.g. heat shock promoters; the promoter for thesmall subunit of RUBISCO; the promoter for the chlorophyll alb bindingprotein) or from plant viruses (e.g. the 35S RNA promoter of CaMV; thecoat protein promoter of TMV) may be used; when cloning in mammaliancell systems, promoters derived from the genome of mammalian cells (e.g.metallothionein promoter) or from mammalian viruses (e.g. the adenoviruslate promoter; the vaccinia virus 7.5 K promoter) may be used; whengenerating cell lines that contain multiple copies of expressionproduct, SV40-, BPV- and EBV-based vectors may be used with anappropriate selectable marker.

In cases where plant expression vectors are used, the expression ofsequences encoding linear or non-cyclized forms of the chimeric proteinsof the invention may be driven by any of a number of promoters. Forexample, viral promoters such as the 35S RNA and 19S RNA promoters ofCaMV (Brisson et al. 1984, Nature 310:511-514), or the coat proteinpromoter of TMV (Takamatsu et al. 1987, EMBO J. 6:307-311) may be used;alternatively, plant promoters such as the small subunit of RUBISCO(Coruzzi et al. 1984, EMBO J. 3:1671-1680; Broglie et al. 1984, Science224:838-843) or heat shock promoters, e.g., soybean hsp17.5-E orhsp17.3-B (Gurley et al. 1986, Mol. Cell. Biol. 6:559-565) may be used.These constructs can be introduced into plant cells using Ti plasmids,Ri plasmids, plant virus vectors, direct DNA transformation,microinjection, electroporation, etc. For reviews of such techniquessee, e.g., Weissbach & Weissbach 1988, Methods for Plant MolecularBiology, Academic Press, NY, Section VIII, pp. 421-463; and Grierson &Corey 1988, Plant Molecular Biology, 2d Ed., Blackie, London, Ch. 7-9.

In one insect expression system that may be used to produce the chimericproteins of the invention, Autographa califormica nuclear polyhidrosisvirus (AcNPV) is used as a vector to express the foreign genes. Thevirus grows in Spodoptera frugiperda cells. A coding sequence may becloned into non-essential regions (for example, the polyhedron gene) ofthe virus and placed under control of an AcNPV promoter (for example,the polyhedron promoter). Successful insertion of a coding sequence willresult in inactivation of the polyhedron gene and production ofnon-occluded recombinant virus (i.e. virus lacking the proteinaceouscoat coded for by the polyhedron gene). These recombinant viruses arethen used to infect Spodoptera frugiperda cells in which the insertedgene is expressed. (see, e.g., Smith et al. 1983, J. Virol. 46:584; U.S.Pat. No. 4,215,051). Further examples of this expression system may befound in Ausubel et al., eds. 1989, Current Protocols in MolecularBiology, Vol. 2, Greene Publish. Assoc. & Wiley Interscience.

Another system which can be used to express the chimeric proteins of theinvention is the glutamine synthetase gene expression system, alsoreferred to as the “GS expression system” (Lonza Biologics PLC,Berkshire UK). This expression system is described in detail in U.S.Pat. No. 5,981,216.

In mammalian host cells, a number of viral based expression systems maybe utilized. In cases where an adenovirus is used as an expressionvector, a coding sequence may be ligated to an adenovirustranscription/translation control complex, e.g., the late promoter andtripartite leader sequence. This chimeric gene may then be inserted inthe adenovirus genome by in vitro or in vivo recombination. Insertion ina non-essential region of the viral genome (e.g. region E1 or E3) willresult in a recombinant virus that is viable and capable of expressingpeptide in infected hosts (see, e.g., Logan & Shenk 1984, Proc. Natl.Acad. Sci. USA 81:3655). Alternatively, the vaccinia 7.5 K promoter maybe used (see, e.g., Mackett et al. 1982, Proc. Natl. Acad. Sci. USA79:7415; Mackett et al. 1984, J. Virol. 49:857; Panicali et al. 1982,Proc. Natl. Acad. Sci. USA 79:4927).

In cases where an adenovirus is used as an expression vector, a codingsequence may be ligated to an adenovirus transcription/translationcontrol complex, e.g., the late promoter and tripartite leader sequence.This chimeric gene may then be inserted in the adenovirus genome by invitro or in vivo recombination. Insertion in a non-essential region ofthe viral genome (e.g. region E1 or E3) will result in a recombinantvirus that is viable and capable of expressing peptide in infected hosts(see, e.g., Logan & Shenk 1984, Proc. Natl. Acad. Sci. USA 81:3655).Alternatively, the vaccinia 7.5 K promoter may be used (see, e.g.,Mackett et al. 1982, Proc. Natl. Acad. Sci. USA 79:7415; Mackett et al.1984, J. Virol. 49:857; Panicali et al. 1982, Proc. Natl. Acad. Sci. USA79:4927).

Host cells containing DNA constructs of the chimeric protein are grownin an appropriate growth medium. As used herein, the term “appropriategrowth medium” means a medium containing nutrients required for thegrowth of cells. Nutrients required for cell growth may include a carbonsource, a nitrogen source, essential amino acids, vitamins, minerals andgrowth factors. Optionally the media can contain bovine calf serum orfetal calf serum. In one embodiment, the media contains substantially noIgG. The growth medium will generally select for cells containing theDNA construct by, for example, drug selection or deficiency in anessential nutrient which is complemented by the selectable marker on theDNA construct or co-transfected with the DNA construct. Culturedmammalian cells are generally grown in commercially availableserum-containing or serum-free media (e.g. MEM, DMEM). Selection of amedium appropriate for the particular cell line used is within the levelof ordinary skill in the art.

The recombinantly produced chimeric protein of the invention can beisolated from the culture media. The culture medium from appropriatelygrown transformed or transfected host cells is separated from the cellmaterial, and the presence of chimeric proteins is demonstrated. Onemethod of detecting the chimeric proteins, for example, is by thebinding of the chimeric proteins or portions of the chimeric proteins toa specific antibody recognizing the chimeric protein of the invention.An anti-chimeric protein antibody may be a monoclonal or polyclonalantibody raised against the chimeric protein in question. For example,the chimeric protein contains at least a portion of an immunoglobulinconstant region. Antibodies recognizing the constant region of manyimmunoglobulins are known in the art and are commercially available. Anantibody can be used to perform an ELISA or a western blot to detect thepresence of the chimeric protein of the invention.

The chimeric protein of the invention can be synthesized in a transgenicanimal, such as a rodent, cow, pig, sheep, or goat. The term “transgenicanimals” refers to non-human animals that have incorporated a foreigngene into their genome. Because this gene is present in germlinetissues, it is passed from parent to offspring. Exogenous genes areintroduced into single-celled embryos (Brinster et al. 1985, Proc. Natl.Acad. Sci. USA 82:4438). Methods of producing transgenic animals areknown in the art, including transgenics that produce immunoglobulinmolecules (Wagner et al. 1981, Proc. Natl. Acad. Sci. USA 78:6376;McKnight et al. 1983, Cell 34:335; Brinster et al. 1983, Nature 306:332;Ritchie et al. 1984, Nature 312:517; Baldassarre et al. 2003,Theriogenology 59:831; Robl et al. 2003, Theriogenology 59:107;Malassagne et al. 2003, Xenotransplantation 10(3):267).

The chimeric protein of the invention can also be produced by acombination of synthetic chemistry and recombinant techniques. Forexample, the portion of an immunoglobulin constant region can beexpressed recombinantly as described above. The biologically activemolecule, can be produced using known chemical synthesis techniques(e.g. solid phase synthesis).

The portion of an immunoglobulin constant region can be ligated to thebiologically active molecule using appropriate ligation chemistry andthen combined with a portion of an immunoglobulin constant region thathas not been ligated to a biologically active molecule to form thechimeric protein of the invention. In one embodiment, the portion of animmunoglobulin constant region is an Fc fragment. The Fc fragment can berecombinantly produced to form Cys-Fc and reacted with a biologicallyactive molecule expressing a thioester to make a monomer-dimer hybrid.In another embodiment, an Fc-thioester is made and reacted with abiologically active molecule expressing an N terminus Cysteine (FIG. 4).

In one embodiment, the portion of an immunoglobulin constant regionligated to the biologically active molecule will form homodimers. Thehomodimers can be disrupted by exposing the homodimers to denaturing andreducing conditions (e.g. beta-mercaptoethanol and 8M urea) and thensubsequently combined with a portion of an immunoglobulin constantregion not linked to a biologically active molecule to formmonomer-dimer hybrids. The monomer-dimer hybrids are then renatured andrefolded by dialyzing into PBS and isolated, e.g., by size exclusion oraffinity chromatography.

In another embodiment, the portion of an immunoglobulin constant regionwill form homodimers before being linked to a biologically activemolecule. In this embodiment, reaction conditions for linking thebiologically active molecule to the homodimer can be adjusted such thatlinkage of the biologically active molecule to only one chain of thehomodimer is favored (e.g. by adjusting the molar equivalents of eachreactant).

The biologically active molecule can be chemically synthesized with an Nterminal cysteine. The sequence encoding a portion of an immunoglobulinconstant region can be sub-cloned into a vector encoding intein linkedto a chitin binding domain (New England Biolabs, Beverly, Mass.). Theintein can be linked to the C terminus of the portion of animmunoglobulin constant region. In one embodiment, the portion of theimmunoglobulin with the intein linked to its C terminus can be expressedin a prokaryotic cell. In another embodiment, the portion of theimmunoglobulin with the intein linked to its C terminus can be expressedin a eukaryotic cell. The portion of immunoglobulin constant regionlinked to intein can be reacted with MESNA. In one embodiment, theportion of an immunoglobulin constant region linked to intein is boundto a column, e.g., a chitin column and then eluted with MESNA. Thebiologically active molecule and portion of an immunoglobulin can bereacted together such that nucleophilic rearrangement occurs and thebiologically active molecule is covalently linked to the portion of animmunoglobulin via an amide bond. (Dawsen et al. 2000, Annu. Rev.Biochem. 69:923). The chimeric protein synthesized this way canoptionally include a linker peptide between the portion of animmunoglobulin and the biologically active molecule. The linker can forexample be synthesized on the N terminus of the biologically activemolecule. Linkers can include peptides and/or organic molecules (e.g.polyethylene glycol and/or short amino acid sequences). This combinedrecombinant and chemical synthesis allows for the rapid screening ofbiologically active molecules and linkers to optimize desired propertiesof the chimeric protein of the invention, e.g., viral inhibition,hemostasis, production of red blood cells, biological half-life,stability, binding to serum proteins or some other property of thechimeric protein. The method also allows for the incorporation ofnon-natural amino acids into the chimeric protein of the invention whichmay be useful for optimizing a desired property of the chimeric proteinof the invention. If desired, the chimeric protein produced by thismethod can be refolded to a biologically active conformation usingconditions known in the art, e.g., reducing conditions and then dialyzedslowly into PBS.

Alternatively, the N-terminal cysteine can be on the portion of animmunoglobulin constant region, e.g., an Fc fragment. An Fc fragment canbe generated with an N-terminal cysteine by taking advantage of the factthat a native Fc has a cysteine at position 226 (see Kabat et al. 1991,Sequences of Proteins of Immunological Interest, U.S. Department ofPublic Health, Bethesda, Md.).

To expose a terminal cysteine, an Fc fragment can be recombinantlyexpressed. In one embodiment, the Fc fragment is expressed in aprokaryotic cell, e.g., E. coli. The sequence encoding the Fc portionbeginning with Cys 226 (EU numbering) can be placed immediatelyfollowing a sequence endcoding a signal peptide, e.g., OmpA, PhoA, STKThe prokaryotic cell can be osmotically shocked to release therecombinant Fc fragment. In another embodiment, the Fc fragment isproduced in a eukaryotic cell, e.g., a CHO cell, a BHK cell. Thesequence encoding the Fc portion fragment can be placed directlyfollowing a sequence encoding a signal peptide, e.g., mouse Igk lightchain or MHC class I Kb signal sequence, such that when the recombinantchimeric protein is synthesized by a eukaryotic cell, the signalsequence will be cleaved, leaving an N terminal cysteine which can thanbe isolated and chemically reacted with a molecule bearing a thioester(e.g. a C terminal thioester if the molecule is comprised of aminoacids).

The N terminal cysteine on an Fc fragment can also be generated using anenzyme that cleaves its substrate at its N terminus, e.g., Factor X^(a),enterokinase, and the product isolated and reacted with a molecule witha thioester.

The recombinantly expressed Fc fragment can be used to make homodimersor monomer-dimer hybrids.

In a specific embodiment, an Fc fragment is expressed with the human ainterferon signal peptide adjacent to the Cys at position 226. When aconstruct encoding this polypeptide is expressed in CHO cells, the CHOcells cleave the signal peptide at two distinct positions (at Cys 226and at Val within the signal peptide 2 amino acids upstream in the Nterminus direction). This generates a mixture of two species of Fcfragments (one with an N-terminal Val and one with an N-terminal Cys).This in turn results in a mixture of dimeric species (homodimers withterminal Val, homodimers with terminal Cys and heterodimers where onechain has a terminal Cys and the other chain has a terminal Val). The Fcfragments can be reacted with a biologically active molecule having a Cterminal thioester and the resulting monomer-dimer hybrid can beisolated from the mixture (e.g. by size exclusion chromatography). It iscontemplated that when other signal peptide sequences are used forexpression of Fc fragments in CHO cells a mixture of species of Fcfragments with at least two different N termini will be generated.

In another embodiment, a recombinantly produced Cys-Fc can form ahomodimer. The homodimer can be reacted with peptide that has a branchedlinker on the C terminus, wherein the branched linker has two C terminalthioesters that can be reacted with the Cys-Fc. In another embodiment,the biologically active molecule has a single non-terminal thioesterthat can be reacted with Cys-Fc. Alternatively, the branched linker canhave two C terminal cysteines that can be reacted with an Fc thioester.In another embodiment, the branched linker has two functional groupsthat can be reacted with the Fc thioester, e.g., 2-mercaptoamine. Thebiologically active molecule may be comprised of amino acids. Thebiologically active molecule may include a small organic molecule or asmall inorganic molecule.

F. Methods of Using Chimeric Proteins

The chimeric proteins of the invention have many uses as will berecognized by one skilled in the art, including, but not limited tomethods of treating a subject with a disease or condition. The diseaseor condition can include, but is not limited to, a viral infection, ahemostatic disorder, anemia, cancer, leukemia, an inflammatory conditionor an autoimmune disease (e.g. arthritis, psoriasis, lupuserythematosus, multiple sclerosis), or a bacterial infection (see, e.g.,U.S. Pat. Nos. 6,086,875, 6,030,613, 6,485,726; WO 03/077834;US2003-0235536A1).

1. Methods of Treating a Subject with a Red Blood Cell Deficiency

The invention relates to a method of treating a subject having adeficiency of red blood cells, e.g., anemia, comprising administering atherapeutically effective amount of at least one chimeric protein,wherein the chimeric protein comprises a first and a second polypeptidechain, wherein the first chain comprises at least a portion of animmunoglobulin constant region and at least one agent capable ofinducing proliferation of red blood cells, e.g., EPO, and the secondpolypeptide chain comprises at least a portion of an immunoglobulinwithout the agent capable of inducing red blood cell proliferation ofthe first chain.

2. Methods of Treating a Subject with a Viral Infection

The invention relates to a method of treating a subject having a viralinfection or exposed to a virus comprising administering atherapeutically effective amount of at least one chimeric protein,wherein the chimeric protein comprises a first and a second polypeptidechain, wherein the first chain comprises at least a portion of animmunoglobulin constant region and at least one antiviral agent, e.g., afusion inhibitor or interferon α and the second polypeptide chaincomprises at least a portion of an immunoglobulin without the antiviralagent of the first chain. In one embodiment, the subject is infectedwith a virus which can be treated with IFNα, e.g., hepatitis C virus. Inone embodiment, the subject is infected with HIV, such as HIV-1 orHIV-2.

In one embodiment, the chimeric protein of the invention inhibits viralreplication. In one embodiment, the chimeric protein of the inventionprevents or inhibits viral entry into target cells, thereby stopping,preventing, or limiting the spread of a viral infection in a subject anddecreasing the viral burden in an infected subject. By linking a portionof an immunoglobulin to a viral fusion inhibitor the invention providesa chimeric protein with viral fusion inhibitory activity with greaterstability and greater bioavailability compared to viral fusioninhibitors alone, e.g., T20, T21, T1249. Thus, in one embodiment, theviral fusion inhibitor decreases or prevents HIV infection of a targetcell, e.g., HIV-1.

a. Conditions That May Be Treated

The chimeric protein of the invention can be used to inhibit or preventthe infection of a target cell by a hepatitis virus, e.g., hepatitisvirus C. The chimeric protein may comprise an anti-viral agent whichinhibits viral replication.

In one embodiment, the chimeric protein of the invention comprises afusion inhibitor. The chimeric protein of the invention can be used toinhibit or prevent the infection of any target cell by any virus (see,e.g., U.S. Pat. Nos. 6,086,875, 6,030,613, 6,485,726; WO 03/077834;US2003-0235536A1). In one embodiment, the virus is an enveloped virussuch as, but not limited to HIV, SW, measles, influenza, Epstein-Barrvirus, respiratory syncytia virus, or parainfluenza virus. In anotherembodiment, the virus is a non-enveloped virus such as rhino virus orpolio virus

The chimeric protein of the invention can be used to treat a subjectalready infected with a virus. The subject can be acutely infected witha virus. Alternatively, the subject can be chronically infected with avirus. The chimeric protein of the invention can also be used toprophylactically treat a subject at risk for contracting a viralinfection, e.g., a subject known or believed to in close contact with avirus or subject believed to be infected or carrying a virus. Thechimeric protein of the invention can be used to treat a subject who mayhave been exposed to a virus, but who has not yet been positivelydiagnosed.

In one embodiment, the invention relates to a method of treating asubject infected with HCV comprising administering to the subject atherapeutically effective amount of a chimeric protein, wherein thechimeric protein comprises an Fc fragment of an IgG and a cytokine,e.g., IFNα.

In one embodiment, the invention relates to a method of treating asubject infected with HIV comprising administering to the subject atherapeutically effective amount of a chimeric protein wherein thechimeric protein comprises an Fc fragment of an IgG and the viral fusioninhibitor comprises T20.

3. Methods of Treating a Subject Having a Hemostatic Disorder

The invention relates to a method of treating a subject having ahemostatic disorder comprising administering a therapeutically effectiveamount of at least one chimeric protein, wherein the chimeric proteincomprises a first and a second chain, wherein the first chain comprisesat least one clotting factor and at least a portion of an immunoglobulinconstant region, and the second chain comprises at least a portion of animmunoglobulin constant region.

The chimeric protein of the invention treats or prevents a hemostaticdisorder by promoting the formation of a fibrin clot. The chimericprotein of the invention can activate any member of a coagulationcascade. The clotting factor can be a participant in the extrinsicpathway, the intrinsic pathway or both. In one embodiment, the clottingfactor is Factor VII or Factor VIIa. Factor VIIa can activate Factor Xwhich interacts with Factor Va to cleave prothrombin to thrombin, whichin turn cleaves fibrinogen to fibrin. In another embodiment, theclotting factor is Factor IX or Factor IXa. In yet another embodiment,the clotting factor is Factor VIII or Factor VIIIa. In yet anotherembodiment, the clotting factor is von Willebrand Factor, Factor XI,Factor XII, Factor V, Factor X or Factor XIII.

a. Conditions that May be Treated

The chimeric protein of the invention can be used to treat anyhemostatic disorder. The hemostatic disorders that may be treated byadministration of the chimeric protein of the invention include, but arenot limited to, hemophilia A, hemophilia B, von Willebrand's disease,Factor XI deficiency (PTA deficiency), Factor XII deficiency, as well asdeficiencies or structural abnormalities in fibrinogen, prothrombin,Factor V, Factor VII, Factor X, or Factor XIII.

In one embodiment, the hemostatic disorder is an inherited disorder. Inone embodiment, the subject has hemophilia A, and the chimeric proteincomprises Factor VIII or Factor VIIIa. In another embodiment, thesubject has hemophilia A and the chimeric protein comprises Factor VIIor Factor VIIa. In another embodiment, the subject has hemophilia B andthe chimeric protein comprises Factor IX or Factor IXa. In anotherembodiment, the subject has hemophilia B and the chimeric proteincomprises Factor VII or Factor VIIa. In another embodiment, the subjecthas inhibitory antibodies to Factor VIII or Factor VIIIa and thechimeric protein comprises Factor VII or Factor VIIa. In yet anotherembodiment, the subject has inhibitory antibodies against Factor IX orFactor IXa and the chimeric protein comprises Factor VII or Factor VIIa.

The chimeric protein of the invention can be used to prophylacticallytreat a subject with a hemostatic disorder. The chimeric protein of theinvention can be used to treat an acute bleeding episode in a subjectwith a hemostatic disorder

In one embodiment, the hemostatic disorder is the result of a deficiencyin a clotting factor, e.g., Factor IX, Factor VIII. In anotherembodiment, the hemostatic disorder can be the result of a defectiveclotting factor, e.g., von Willebrand's Factor.

In another embodiment, the hemostatic disorder can be an acquireddisorder. The acquired disorder can result from an underlying secondarydisease or condition. The unrelated condition can be, as an example, butnot as a limitation, cancer, an autoimmune disease, or pregnancy. Theacquired disorder can result from old age or from medication to treat anunderlying secondary disorder (e.g. cancer chemotherapy).

4. Methods of Treating a Subject in Need of a General Hemostatic Agent

The invention also relates to methods of treating a subject that doesnot have a hemostatic disorder or a secondary disease or conditionresulting in acquisition of a hemostatic disorder. The invention thusrelates to a method of treating a subject in need of a generalhemostatic agent comprising administering a therapeutically effectiveamount of at least one chimeric protein, wherein the chimeric proteincomprises a first and a second polypeptide chain wherein the firstpolypeptide chain comprises at least a portion of an immunoglobulinconstant region and at least one clotting factor and the second chaincomprises at least a portion of an immunoglobulin constant regionwithout the clotting factor of the first polypeptide chain.

a. Conditions that May be Treated

In one embodiment, the subject in need of a general hemostatic agent isundergoing, or is about to undergo, surgery. The chimeric protein of theinvention can be administered prior to or after surgery as aprophylactic. The chimeric protein of the invention can be administeredduring or after surgery to control an acute bleeding episode. Thesurgery can include, but is not limited to, liver transplantation, liverresection, or stem cell transplantation.

The chimeric protein of the invention can be used to treat a subjecthaving an acute bleeding episode who does not have a hemostaticdisorder. The acute bleeding episode can result from severe trauma,e.g., surgery, an automobile accident, wound, laceration gun shot, orany other traumatic event resulting in uncontrolled bleeding.

5. Treatment Modalities

The chimeric protein of the invention can be administered intravenously,subcutaneously, intra-muscularly, or via any mucosal surface, e.g.,orally, sublingually, buccally, sublingually, nasally, rectally,vaginally or via pulmonary route. The chimeric protein can be implantedwithin or linked to a biopolymer solid support that allows for the slowrelease of the chimeric protein to the desired site.

The dose of the chimeric protein of the invention will vary depending onthe subject and upon the particular route of administration used.Dosages can range from 0.1 to 100,000 μg/kg body weight. In oneembodiment, the dosing range is 0.1-1,000 μg/kg. The protein can beadministered continuously or at specific timed intervals. In vitroassays may be employed to determine optimal dose ranges and/or schedulesfor administration. Many in vitro assays that measure viral infectivityare known in the art. For example, a reverse transcriptase assay, or anrt PCR assay or branched DNA assay can be used to measure HIVconcentrations. A StaClot assay can be used to measure clottingactivity. Additionally, effective doses may be extrapolated fromdose-response curves obtained from animal models.

The invention also relates to a pharmaceutical composition comprising aviral fusion inhibitor, at least a portion of an immunoglobulin and apharmaceutically acceptable carrier or excipient. Examples of suitablepharmaceutical carriers are described in Remington PharmaceuticalSciences by E. W. Martin. Examples of excipients can include starch,glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silicagel, sodium stearate, glycerol monostearate, talc, sodium chloride,dried skim milk, glycerol, propylene, glycol, water, ethanol, and thelike. The composition can also contain pH buffering reagents, andwetting or emulsifying agents.

For oral administration, the pharmaceutical composition can take theform of tablets or capsules prepared by conventional means. Thecomposition can also be prepared as a liquid for example a syrup or asuspension. The liquid can include suspending agents (e.g. sorbitolsyrup, cellulose derivatives or hydrogenated edible fats), emulsifyingagents (lecithin or acacia), non-aqueous vehicles (e.g. almond oil, oilyesters, ethyl alcohol, or fractionated vegetable oils), andpreservatives (e.g. methyl or propyl-p-hydroxybenzoates or sorbic acid).The preparations can also include flavoring, coloring and sweeteningagents. Alternatively, the composition can be presented as a dry productfor constitution with water or another suitable vehicle.

For buccal and sublingual administration the composition may take theform of tablets, lozenges or fast dissolving films according toconventional protocols.

For administration by inhalation, the compounds for use according to thepresent invention are conveniently delivered in the form of an aerosolspray from a pressurized pack or nebulizer (e.g. in PBS), with asuitable propellant, e.g., dichlorodifluoromethane,trichlorofluoromethane, dichlorotetrafluoromethane, carbon dioxide orother suitable gas. In the case of a pressurized aerosol the dosage unitcan be determined by providing a valve to deliver a metered amount.Capsules and cartridges of, e.g., gelatin for use in an inhaler orinsufflator can be formulated containing a powder mix of the compoundand a suitable powder base such as lactose or starch.

The pharmaceutical composition can be formulated for parenteraladministration (i.e. intravenous or intramuscular) by bolus injection.Formulations for injection can be presented in unit dosage form, e.g.,in ampoules or in multidose containers with an added preservative. Thecompositions can take such forms as suspensions, solutions, or emulsionsin oily or aqueous vehicles, and contain formulatory agents such assuspending, stabilizing and/or dispersing agents. Alternatively, theactive ingredient can be in powder form for constitution with a suitablevehicle, e.g., pyrogen free water.

The pharmaceutical composition can also be formulated for rectaladministration as a suppository or retention enema, e.g., containingconventional suppository bases such as cocoa butter or other glycerides.

6. Combination Therapy

The chimeric protein of the invention can be used to treat a subjectwith a disease or condition in combination with at least one other knownagent to treat said disease or condition.

In one embodiment, the invention relates to a method of treating asubject infected with HIV comprising administering a therapeuticallyeffective amount of at least one chimeric protein comprising a first anda second chain, wherein the first chain comprises an HIV fusioninhibitor and at least a portion of an immunoglobulin constant regionand the second chain comprises at least a portion of an immunoglobulinwithout an HIV fusion inhibitor of the first chain, in combination withat least one other anti-HIV agent. Said other anti-HIV agent can be anytherapeutic with demonstrated anti-HIV activity. Said other anti-HIVagent can include, as an example, but not as a limitation, a proteaseinhibitor (e.g. Amprenavie®, Crixivan®, Ritonivir®), a reversetranscriptase nucleoside analog (e.g. AZT, DDI, D4T, 3TC, Ziagen®), anonnucleoside analog reverse transcriptase inhibitor (e.g. Sustiva®),another HIV fusion inhibitor, a neutralizing antibody specific to HIV,an antibody specific to CD4, a CD4 mimic, e.g., CD4-IgG2 fusion protein(U.S. patent application Ser. No. 09/912,824) or an antibody specific toCCR5, or CXCR4, or a specific binding partner of CCR5, or CXCR4.

In another embodiment, the invention relates to a method of treating asubject with a hemostatic disorder comprising administering atherapeutically effective amount of at least one chimeric proteincomprising a first and a second chain, wherein the first chain comprisesat least one clotting factor and at least a portion of an immunoglobulinconstant region and the second chain comprises at least a portion of animmunoglobulin constant region without the clotting factor of the firstchain, in combination with at least one other clotting factor or agentthat promotes hemostasis. Said other clotting factor or agent thatpromotes hemostasis can be any therapeutic with demonstrated clottingactivity. As an example, but not as a limitation, the clotting factor orhemostatic agent can include Factor V, Factor VII, Factor VIII, FactorIX, Factor X, Factor XI, Factor XII, Factor XIII, prothrombin, orfibrinogen or activated forms of any of the preceding. The clottingfactor of hemostatic agent can also include anti-fibrinolytic drugs,e.g., epsilon-amino-caproic acid, tranexamic acid.

7. Methods of Inhibiting Viral Fusion with a Target Cell

The invention also relates to an in vitro method of inhibiting HIVfusion with a mammalian cell comprising combining the mammalian cellwith at least one chimeric protein, wherein the chimeric proteincomprises a first and a second chain, wherein the first chain comprisesat least a portion of an immunoglobulin constant region and an HIVinhibitor and the second chain comprises at least a portion of animmunoglobulin constant region without the HIV inhibitor of the firstchain. The mammalian cell can include any cell or cell line susceptibleto infection by HIV including but not limited to primary human CD4⁺ Tcells or macrophages, MOLT-4 cells, CEM cells, AA5 cells or HeLa cellswhich express CD4 on the cell surface.

G. Methods of Isolating Chimeric Proteins

Typically, when chimeric proteins of the invention are produced they arecontained in a mixture of other molecules such as other proteins orprotein fragments. The invention thus provides for methods of isolatingany of the chimeric proteins described supra from a mixture containingthe chimeric proteins. It has been determined that the chimeric proteinsof the invention bind to dye ligands under suitable conditions and thataltering those conditions subsequent to binding can disrupt the bondbetween the dye ligand and the chimeric protein, thereby providing amethod of isolating the chimeric protein. In some embodiments themixture may comprise a monomer-dimer hybrid, a dimer and at least aportion of an immunoglobulin constant region, e.g., an Fc. Thus, in oneembodiment, the invention provides a method of isolating a monomer-dimerhybrid. In another embodiment, the invention provides a method ofisolating a dimer.

Accordingly, in one embodiment, the invention provides a method ofisolating a monomer-dimer hybrid from a mixture, where the mixturecomprises

a) the monomer-dimer hybrid comprising a first and second polypeptidechain,

wherein the first chain comprises a biologically active molecule, and atleast a portion of an immunoglobulin constant region and wherein thesecond chain comprises at least a portion of an immunoglobulin constantregion without a biologically active molecule or immunoglobulin variableregion;

b) a dimer comprising a first and second polypeptide chain, wherein thefirst and second chains both comprise a biologically active molecule,and at least a portion of an immunoglobulin constant region; and

c) a portion of an immunoglobulin constant region; said methodcomprising

-   -   1) contacting the mixture with a dye ligand linked to a solid        support under suitable conditions such that both the        monomer-dimer hybrid and the dimer bind to the dye ligand;    -   2) removing the unbound portion of an immunoglobulin constant        region;    -   3) altering the suitable conditions of 1) such that the binding        between the monomer-dimer hybrid and the dye ligand linked to        the solid support is disrupted;    -   4) isolating the monomer-dimer hybrid.        In some embodiments, prior to contacting the mixture with a dye        ligand, the mixture may be contacted with a chromatographic        substance such as protein A sepharose or the like. The mixture        is eluted from the chromatographic substance using an        appropriate elution buffer (e.g. a low pH buffer) and the eluate        containing the mixture is then contacted with the dye ligand.

Suitable conditions for contacting the mixture with the dye ligand mayinclude a buffer to maintain the mixture at an appropriate pH. Anappropriate pH may include a pH of from, 3-10, 4-9, 5-8. In oneembodiment, the appropriate pHis 8.0. Any buffering agent known in theart may be used so long as it maintains the pH in the appropriate range,e.g., tris, HEPES, PIPES, MOPS. Suitable conditions may also include awash buffer to elute unbound species from the dye ligand. The washbuffer may be any buffer which does not disrupt binding of a boundspecies. For example, the wash buffer can be the same buffer used in thecontacting step.

Once the chimeric protein is bound to the dye ligand, the chimericprotein is isolated by altering the suitable conditions. Altering thesuitable conditions may include the addition of a salt to the buffer.Any salt may be used, e.g., NaCl, KCl. The salt should be added at aconcentration that is high enough to disrupt the binding between the dyeligand and the desired species, e.g., a monomer-dimer hybrid.

In some embodiments where the mixture is comprised of an Fc, amonomer-dimer hybrid, and a dimer, it has been found that the Fc doesnot bind to the dye ligand and thus elutes with the flow through. Thedimer binds more tightly to the dye ligand than the monomer-dimerhybrid. Thus a higher concentration of salt is required to disrupt thebond (e.g. elute) between the dimer and the dye ligand compared to thesalt concentration required to disrupt the bond between the dye ligandand the monomer-dimer hybrid.

In some embodiments NaCl may be used to isolate the monomer-dimer hybridfrom the mixture. In some embodiments the appropriate concentration ofsalt which disrupts the bond between the dye ligand and themonomer-dimer hybrid is from 200-700 mM, 300-600 mM, 400-500 mM. In oneembodiment, the concentration of NaCl required to disrupt the bindingbetween the dye ligand the monomer-dimer hybrid is 400 mM.

NaCl may also be used to isolate the dimer from the mixture. Typically,the monomer-dimer hybrid is isolated from the mixture before the dimer.The dimer is isolated by adding an appropriate concentration of salt tothe buffer, thereby disrupting the binding between the dye ligand andthe dimer. In some embodiments the appropriate concentration of saltwhich disrupts the bond between the dye ligand and the dimer is from 800mM to 2 M, 900 mM to 1.5 M, 950 mM to 1.2 M. In one specific embodiment,1 M NaCl is used to disrupt the binding between the dye ligand and thedimer.

The dye ligand may be a bio-mimetic. A bio- a human-made substance,device, or system that imitates nature. Thus in some embodiments the dyeligand imitates a molecule's naturally occurring ligand. The dye ligandmay be chosen from Mimetic Red™, Mimetic Red 2™, Mimetic Orange 1™,Mimetic Orange 2™, Mimetic Orange 3™, Mimetic Yellow 1™, Mimetic Yellow2™, Mimetic Green 1™, Mimetic Blue 1™, and Mimetic Blue 2™ (PrometicBiosciences (USA) Inc., Wayne, N.J.). In one specific embodiment, thedye ligand is Mimetic Red 2™ (Prometic Biosciences (USA) Inc., Wayne,N.J.). In certain embodiments the dye ligand is linked to a solidsupport, e.g., from Mimetic Red 1A6XL™, Mimetic Red 2 A6XL™, MimeticOrange 1 A6XL™, Mimetic Orange 2 A6XL™, Mimetic Orange 3 A6XL™, MimeticYellow 1 A6XL™, Mimetic Yellow 2 A6XL™, Mimetic Green 1 A6XL™, MimeticBlue 1 A6XL™, and Mimetic Blue 2 A6XL™ (Prometic Biosciences (USA) Inc.,Wayne, N.J.).

The dye ligand may be linked to a solid support. The solid support maybe any solid support known in the art (see, e.g.,www.seperationsNOW.com). Examples of solid supports may include a bead,a gel, a membrane, a nanoparticle, or a microsphere. The solid supportmay comprise any material which can be linked to a dye ligand (e.g.agarose, polystyrene, sepharose, sephadex). Solid supports may compriseany synthetic organic polymer such as polyacrylic, vinyl polymers,acrylate, polymethacrylate, and polyacrylamide. Solid supports may alsocomprise a carbohydrate polymer, e.g., agarose, cellulose, or dextran.Solid supports may comprise inorganic oxides, such as silica, zirconia,titania, ceria, alumina, magnesia (i.e., magnesium oxide), or calciumoxide. Solid supports may also comprise combinations of some of theabove-mentioned supports including, but not limited to,dextran-acrylamide.

EXAMPLES Example 1 Molecular Weight Affects FcRn Mediated Trancvtosis

Chimeric proteins comprised of various proteins of interest and IgG Fcwere recombinantly produced (Sambrook et al. Molecular Cloning: ALaboratory Manual, 2 ed., Cold Spring Harbor Laboratory Press, (1989))or in the case of contactin-Fc, MAB-β-gal, (a complex of a monoclonalantibody bound to 13-gal) (Biodesign International, Saco, Me.) andMAB-GH (a complex of monoclonal antibody and growth hormone)(ResearchDiagnostics, Inc. Flanders, N.J.) were purchased commercially. Briefly,the genes encoding the protein of interest were cloned by PCR, and thensub-cloned into an Fc fusion expression plasmid. The plasmids weretransfected into DG44 CHO cells and stable transfectants were selectedand amplified with methotrexate. The chimeric protein homodimers werepurified over a protein A column. The proteins tested includedinterferon α, growth hormone, erythropoietin, follicle stimulatinghormone, Factor IX, beta-galactosidase, contactin, and Factor VIIILinking the proteins to immunoglobulin portions, including the FcRnreceptor binding partner, or using commercially available whole antibody(including the FcRn binding region)-antigen complexes permitted theinvestigation of transcytosis as a function of molecular weight (seeU.S. Pat. No. 6,030,613). The chimeric proteins were administered torats orally and serum levels were measured 2-4 hours post administrationusing an ELISA for recombinantly produced chimeric proteins and both awestern blot and ELISA for commercially obtained antibody complexes andchimeric proteins. Additionally, all of the commercially obtainedproteins or complexes as well as Factor VIII-Fc, Factor IX-Fc and Epo-Fccontrols were iodinated using IODO beads (Pierce, Pittsburgh, Pa.). Theresults indicated serum levels of Fc and monoclonal antibody chimericproteins orally administered to rats are directly related to the size ofthe protein. The apparent cutoff point for orally administered Fcchimeric proteins is between 200-285 kD. (Table 2).

TABLE 2 Protein Size (kD) Transcytosis IFNα-Fc 92 ++++ GH-Fc 96 +++Epo-Fc 120 +++ FSH-Fc 170 +++ MAB:GH 172-194 +++ FIX-Fc 200 + MAB:βGal285-420 − Contactin-Fc 300 − FVIIIΔ-Fc 380 −

Example 2 Cloning of pcDNA 3.1-Flag-Fc

The sequence for the FLAG peptide (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys; SEQID NO: 91), a common affinity tag used to identify or purify proteins,was cloned into the pcDNA 3.1-Fc plasmid, which contains the mouse Igksignal sequence followed by the Fc fragment of human IgG1 (amino acids221-447, EU numbering). The construct was created by overlapping PCRusing the following primers:

FlagFc-F1: (SEQ ID NO: 41) 5′-GCTGGCTAGCCACCATGGA-3′ FlagFc-R1:(SEQ ID NO: 42) 5′-CTTGTCATCGTCGTCCTTGTAGTCGTCA CCAGTGGAACCTGGAAC-3′FlagFc-F2: (SEQ ID NO: 43)5′-GACTACAAGG ACGACGATGA CAAGGACAAA ACTCACACATGCCCACCGTG CCCAGCTCCG GAACTCC-3′ FlagFc-R2: (SEQ ID NO: 44)5′-TAGTGGATCCTCATTTACCCG-3′

The pcDNA 3.1-Fc template was then added to two separate PCR reactionscontaining 50 pmol each of the primer pairs FlagFc-F1/R1 or FlagFc-F2/R2in a 50 μl reaction using Pfu Ultra DNA polymerase (Stratagene, Calif.)according to manufacturer's standard protocol in a MJ Thermocycler usingthe following cycles: 95° C. 2 minutes; 30 cycles of (95° C. 30 seconds,52° C. 30 seconds, 72° C. 45 seconds), followed by 72° C. for 10minutes. The products of these two reactions were then mixed in anotherPCR reaction (2 μl each) with 50 pmol of FlagFc-F1 and FlagFc-R2 primersin a 50 μl reaction using Pfu Ultra DNA polymerase (Stratagene, Calif.)according to manufacturer's standard protocol in a MJ Thermocycler usingthe following cycles: 95° C. 2 minutes; 30 cycles of (95QC 30 seconds,52° C. 30 seconds, 72° C. 45 seconds), followed by 72° C. for 10minutes. The resulting fragment was gel purified, digested and insertedinto the pcDNA 3.1-Fc plasmid NheI-Bam HI. The resulting plasmidcontains contains the mouse Iv signal sequence producing the FlagFcprotein.

Example 3 Cloning of -Factor VII-Fc Construct

The coding sequence for Factor VII, was obtained by RT-PCR from humanfetal liver RNA (Clontech, Palo Alto, Calif.). The cloned region iscomprised of the cDNA sequence from by 36 to by 1430 terminating justbefore the stop codon. A SbfI site was introduced on the N-terminus. ABspEI site was introduced on the C-terminus. The construct was cloned byPCR using the primers:

Downstream: (SEQ ID NO: 45) 5′ GCTACCTGCAGGCCACCATGGTCTCCCAGGCCCTCAGG 3′Upstream: (SEQ ID NO: 46) 5′ CAGTTCCGGAGCTGGGCACGGCGGGCACGTGTGAGTTTTGTCGGGAAAT GG 3′and the following conditions: 95° C. for 5 minutes followed by 30 cyclesof 95° C. for 30 seconds, 55° C. for 30 seconds, 72° C. for 1 minute and45 seconds, and a final extension cycle of 72° C. for 10 minutes.

The fragment was digested SbfI-BspE I and inserted into pED.dC-Fc aplasmid encoding for the Fc fragment of an IgG1.

Example 4 Cloning of Factor IX-Fc Construct

The human Factor IX coding sequence, including the prepropeptidesequence, was obtained by RT-PCR amplification from adult human liverRNA using the following primers:

natFIX-F: (SEQ ID NO: 47) 5′-TTACTGCAGAAGGTTATGCAGCGCGTGAACATG-3′ F9-R:(SEQ ID NO: 48) 5′-TTTTTCGAATTCAGTGAGCTTTGTTTTTTCCTTAATCC-3′

20 ng of adult human liver RNA (Clontech, Palo Alto, Calif.) and 25 pmoleach primer were added to a RT-PCR reaction using the SuperScript.™One-Step RT-PCR with PLATINUM® Taq system Onvitrogen, Carlsbad, Calif.)according to manufacturers protocol. Reaction was carried out in a MJThermocycler using the following cycles: 50° C. 30 minutes; 94° C. 2minutes; 35 cycles of (94° C. 30 seconds, 58° C. 30 seconds, 72° C. 1minute), and a final 72° C. 10 minutes. The fragment was gel purifiedusing Qiagen Gel Extraction Kit (Qiagen, Valencia, Calif.), and digestedwith PstI-EcoRI, gel purified, and cloned into the corresponding digestof the pED.dC.XFc plasmid.

Example 5 Cloning of PACE Construct

The coding sequence for human PACE (paired basic amino acid cleavingenzyme), an endoprotease, was obtained by RT-PCR. The following primerswere used:

PACE-F1: (SEQ ID NO: 49) 5′-GGTAAGCTTGCCATGGAGCTGAGGCCCTGGTTGC-3′PACE-R1: (SEQ ID NO: 50) 5′-GTTTTCAATCTCTAGGACCCACTCGCC-3′ PACE-F2:(SEQ ID NO: 51) 5′-GCCAGGCCACATGACTACTCCGC-3′ PACE-R2: (SEQ ID NO: 52)5′-GGTGAATTCTCACTCAGGCAGGTGTGAGGGCAGC-3′

The PACE-F1 primer adds a HindIII site to the 5′ end of the PACEsequence beginning with 3 nucleotides before the start codon, while thePACE-R2 primer adds a stop codon after amino acid 715, which occurs atthe end of the extracellular domain of PACE, as well as adding an EcoRIsite to the 3′ end of the stop codon. The PACE-R1 and -F2 primers annealon the 3′ and 5′ sides of an internal BamHI site, respectively. TwoRT-PCR reactions were then set up using 25 pmol each of the primer pairsof PACE-F1/R1 or PACE-F2/R2 with 20 ng of adult human liver RNA(Clontech; Palo Alto, Calif.) in a 50 μl RT-PCR reaction using theSuperScript.™ One-Step RT-PCR with PLATINUM® Taq system (Invitrogen,Carlsbad, Calif.) according to manufacturers protocol. The reaction wascarried out in a MJ Thermocycler using the following cycles: 50° C. 30minutes; 94° C. 2 minutes; 30 cycles of (94° C. 30 seconds, 58° C. 30seconds, 72° C. 2 minutes), followed by 72° C. 10 minutes. Thesefragments were each ligated into the vector pGEM T-Easy (Promega,Madison, Wis.) and sequenced fully. The F2-R2 fragment was thensubcloned into pcDNA6 V5/His (Invitrogen, Carlsbad, Calif.) using theBamHI/EcoRI sites, and then the F1-R1 fragment was cloned into thisconstruct using the HindIII/BamHI sites. The final plasmid, pcDNA6-PACE,produces a soluble form of PACE (amino acids 1-715), as thetransmembrane region has been deleted. The sequence of PACE inpcDNA6-PACE is essentially as described in Harrison et al. 1998,Seminars in Hematology 35:4.

Example 6 Cloning of IFNα-Fc Eight Amino Acid Linker Construct

The human interferon α 2b (hIFNα) coding sequence, including the signalsequence, was obtained by PCR from human genomic DNA using the followingprimers:

IFNa-Sig-F: (SEQ ID NO: 53) 5′-GCTACTGCAGCCACCATGGCCTTGACCTTTGCTTTAC-3′IFNa-EcoR-R: (SEQ ID NO: 54) 5′-CGTTGAATTCTTCCTTACTTCTTAAACTTTCTTGC-3′

Genomic DNA was prepared from 373MG human astrocytoma cell line,according to standard methods (Sambrook et al. 1989, Molecular Cloning:A Laboratory Manual, 2d ed., Cold Spring Harbor Laboratory Press).Briefly, approximately 2×10⁵ cells were pelleted by centrifugation,resuspended in 100 μl phosphate buffered saline pH 7.4, then mixed withan equal volume of lysis buffer (100 mM Tris pH 8.0/200 mM NaCl/2% SDS/5mM EDTA). Proteinase K was added to a final concentration of 100 μg/ml,and the sample was digested at 37° C. for 4 hours with occasional gentlemixing. The sample was then extracted twice with phenol: chloroform, theDNA precipitated by adding sodium acetate pH 7.0 to 100 mM and an equalvolume of isopropanol, and pelleted by centrifugation for 10 min at roomtemperature. The supernatant was removed and the pellet was washed oncewith cold 70% ethanol and allowed to air dry before resuspending in TE(10 mM Tris pH 8.0/1 mM EDTA).

100 ng of this genomic DNA was then used in a 25 μl PCR reaction with 25pmol of each primer using Expand High Fidelity System (BoehringerMannheim, Indianapolis, Ind.) according to manufacturer's standardprotocol in a MJ Thermocycler using the following cycles: 94° C. 2minutes; 30 cycles of (94° C. 30 seconds, 50° C. 30 seconds, 72° C. 45seconds), and finally 72° C. 10 minutes. The expected sized band (˜550bp) was gel purified with a Gel Extraction kit (Qiagen, Valencia,Calif.), digested with PstI/EcoRI, gel purified again, and cloned intothe PstI/EcoRI site of pED.dC.XFc, which contains an 8 amino acid linker(EFAGAAAV; SEQ ID NO: 31) followed by the Fc region of human IgG1.

Example 7 Cloning of IFNα Fc Δ Linker Construct

1 μg of purified pED.dC.native human IFNαFc DNA, from Example 6, wasthen used as a template in a 25 μl PCR reaction with 25 pmol of eachprimer IFNa-Sig-F and the following primer:

hIFNaNoLinkFc-R: (SEQ ID NO: 55) 5′CAGTTCCGGAGCTGGGCACGGCGGGCACGTGTGAGITTIGTOTTCCTTACTTCTTAAACTTTTTGCAAGTTT G- 3′

The PCR reaction was carried out using Expand High Fidelity System(Boehringer Mannheim, Indianapolis, Ind.) according to themanufacturer's standard protocol in a RapidCycler thermocycler (IdahoTechnology, Salt Lake City, Utah), denaturing at 94° C. for 2 minutesfollowed by 18 cycles of 95° C. for 15 seconds, 55° C. for 0 seconds,and 72° C. for 1 minute with a slope of 6, followed by 72° C. extensionfor 10 minutes. A PCR product of the correct size (˜525 bp) was gelpurified using a Gel Extraction kit (Qiagen; Valencia, Calif.), digestedwith the PstI and BspEI restriction enzymes, gel purified, and subclonedinto the corresponding sites of a modified pED.dC.XFc, where amino acids231-233 of the Fc region were altered using the degeneracy of thegenetic code to incorporate a BspEI site while maintaining the wild typeamino acid sequence.

Example 8 Cloning of IFNα Fc GS15 Linker Construct

A new backbone vector was created using the Fc found in the Δlinkerconstruct (containing BspEI and RsrII sites in the 5′ end using thedegeneracy of the genetic code to maintain the amino acid sequence),using this DNA as a template for a PCR reaction with the followingprimers:

5′ B2xGGGGS (SEQ ID NO: 86): (SEQ ID NO: 56) 5′gtcaggatccggcggtggagggagcgacaaaactcacacgtgccc 3′ 3′GGGGS (SEQ ID NO: 81): (SEQ ID NO: 57) 5′tgacgcggccgctcatttacccggagacaggg 3′

A PCR reaction was carried out with 25 pmol of each primer using PfuTurbo enzyme (Stratagene, La Jolla, Calif.) according to manufacturer'sstandard protocol in a MJ Thermocycler using the following method: 95°C. 2 minutes; 30 cycles of (95° C. 30 seconds, 54° C. 30 seconds, 72° C.2 minutes), 72° C. 10 minutes. The expected sized band (˜730 bp) was gelpurified with a Gel Extraction kit (Qiagen, Valencia Calif.), digestedBamHI/NotI; gel purified again, and cloned into the BamHI/NotI digestedvector of pcDNA6 ID, a version of pcDNA6 with the IRES sequence and dhfrgene inserted into NotI/XbaI site.

500 ng of purified pED.dC.native human IFNαFc DNA was then used as atemplate in a 25 μl PCR reaction with the following primers:

5′ IFNa for GGGGS (SEQ ID NO: 81): (SEQ ID NO: 58) 5′ccgctagcctgcaggccaccatggccttgacc 3′ 3′ IFNa for GGGGS (SEQ ID NO: 81):(SEQ ID NO: 59) 5′ ccggatccgccgccaccttccttactacgtaaac 3′

A PCR reaction was carried out with 25 pmol of each primer using ExpandHigh Fidelity System (Boehringer Mannheim, Indianapolis, Ind.) accordingto manufacturer's standard protocol in a MJ Thermocycler using thefollowing cycles: 95° C. 2 minutes; 14 cycles of (94° C. 30 seconds, 48°C. 30 seconds, 72° C. 1 minute), 72° C. 10 minutes. The expected sizedband (˜600 bp) was gel purified with a Gel Extraction kit (Qiagen,Valencia Calif.), digested NheI/BamHI, gel purified again, and clonedinto the NheI/BamHI site of the pcDNA6 ID/Fc vector, above, to create anIFNα Fc fusion with a 10 amino acid Gly/Ser linker (2×GGGGS; SEQ ID NO:86), pcDNA6 ID/IFNα-GS10-Fc.

A PCR reaction was then performed using 500 ng of this pcDNA6 ID/IFNα-GS10-Fc with the following primers

(SEQ ID NO: 60) 5′ B3XGGGGS:5′ (SEQ ID NO: 61)gtcaggatccggtggaggcgggtccggcggtggagggagcgacaaaactcacacgtgccc 3′ fcclv-R:(SEQ ID NO: 62) 5′ atagaagcctttgaccaggc 3′

A PCR reaction was carried out with 25 pmol of each primer using ExpandHigh Fidelity System (Boehringer Mannheim, Indianapolis, Ind.) accordingto manufacturer's standard protocol in a MJ Thermocycler using thefollowing cycles: 95° C. 2 minutes; 14 cycles of (94° C. 30 seconds, 48°C. 30 seconds, 72° C. 1 minute), 72° C. 10 minutes. The expected sizedband (504 bp) was gel purified with a Gel Extraction kit (Qiagen,Valencia Calif.), digested BamHI/BspEI, the 68 bp band was gel purified,and cloned into the BamHI/BspEI site of the pcDNA6 ID/IFNα-GS 10-Fcvector, above, to create an IFNα Fc fusion with a 15 amino acid Gly/Serlinker (3×ggggs; SEQ ID NO: 60), pcDNA6 ID/IFNα-G515-Fc.

Example 9 Cloning of a Basic Peptide Construct

The hinge region of the human IgG1 Fc fragment from amino acid 221-229(EU numbering) was replaced with a basic peptide (CCB).

Four overlapping oligos were used (IDT, Coralville, Iowa):

1. CCB-Fc Sense 1: (SEQ ID NO: 63) 5′GCC GGC GAA TTC GGT GGT GAG TAC CAG GCC CTG AAG AAG AAG GTG GCCCAG CTG AAG GCC AAG AAC CAG GCC CTG AAG AAG AAG 3′ 2. CCB-Fc Sense 2:(SEQ ID NO: 64) 5′GTG GCC CAG CTG AAG CAC AAG GGC GGC GGC CCC GCC CCA GAG CTC CTGGGC GGA CCG A 3′ 3. CCB-Fc Anti-Sense 1: (SEQ ID NO: 65) 5′CGG TCC GCC CAG GAG CTC TGG GGC GGG GCC GCC GCC CTT GTG CTT CAGCTG GGC CAC CTT CTT CTT CAG GGC CTG GTT CTT G 3′ 4. CCB-Fc Anti-Sense 2:(SEQ ID NO: 66) 5′GCC TTC AGC TGG GCC ACC TTC TTC TTC AGG GCC TGG TAC TCA CCA CCGAAT TCG CCG GCA 3′

The oligos were reconstituted to a concentration of 50 μM with dH₂O. 5μl of each oligo were annealed to each other by combining in a thinwalled PCR tube with 2.2 μl of restriction buffer #2 (i.e. finalconcentration of 10 mM Tris HCl pH 7.9, 10 mM MgCl₂, 50 mM Na CI, 1 mMdithiothreitol) (New England Biolabs, Beverly, Mass.) and heated to 95°C. for 30 seconds and then allowed to anneal by cooling slowly for 2hours to 25° C. 5 pmol of the now annealed oligos were ligated into apGEM T-Easy vector as directed in the kit manual. (Promega, MadisonWis.). The ligation mixture was added to 50 μl of DH5α competent E. coliceel's (Invitrogen, Carlsbad, Calif.) on ice for 2 minutes, incubated at37° C. for 5 minutes, incubated on ice for 2 minutes, and then plated onLB+100 μg/ampicillin agar plates and placed at 37° C. for 14 hours.Individual bacterial colonies were picked and placed in 5 nil of LB+100μg/L ampicillin and allowed to grow for 14 hours. The tubes were spundown at 2000×g, 4° C. for 15 minutes and the vector DNA was isolatedusing Qiagen miniprep kit (Qiagen, Valencia, Calif.) as indicated in thekit manual. 2 μg of DNA was digested with NgoM IV-Rsr-II. The fragmentwas gel purified by the Qiaquick method as instructed in the kit manual(Qiagen, Valencia, Calif.) and ligated to pED.dcEpoFc with NgoM IV/RsrII. The ligation was transformed into DH5α competent E. coli cells andthe DNA prepared as described for the pGEM T-Easy vector.

Example 10 Cloning of the Ervthropoietin-Acidic Peptide Fc Construct

The hinge region of the human IgG1 Fc fragment in EPO-Fc from amino acid221-229 (EU numbering) was replaced with an acidic peptide (CCA). Fouroverlapping oligos were used (IDT, Coralville, Iowa):

1. Epo-CCA-Fc Sense 1: (SEQ ID NO: 67) 5′CCG GTG ACA GGG AAT TCG GTG GTG AGT ACC AGG CCC TGG AGA AGG AGGTGG CCC AGC TGG AG 3′ 2. Epo-CCA-Fc Sense 2: (SEQ ID NO: 68) 5′GCC GAG AAC CAG GCC CTG GAG AAG GAG GTG GCC CAG CTG GAG CACGAG GGT GGT GGT CCC GCT CCA GAG CTG CTG GGC GGA CA 3′3. Epo-CCA-Fc Anti-Sense 1: (SEQ ID NO: 69) 5′GTC CGC CCA GCA GCT CTG GAG CGG GAC CAC CAC CCT CGT GCT CCA GCTGGG CCA C 3′ 4. Epo-CCA-Fc Anti-Sense 2: (SEQ ID NO: 70) 5′CTC CTT CTC CAG GGC CTG GTT CTC GGC CTC CAG CTG GGC CAC CTC CTT CTCCAG GGC CTG GTA CTC ACC ACC GAA TTC CCT GTC ACC GGA 3′

The oligos were reconstituted to a concentration of 50 μM with dH₂O. 5μl of each oligo were annealed to each other by combining in a thinwalled PCR tube with 2.2 μl of restriction buffer No. 2 (New EnglandBiolabs, Beverly, Mass.) and heated to 95° C. for 30 seconds and thenallowed to cool slowly for 2 hours to 25° C. 5 pmol of the now annealedoligos were ligated into a pGEM T-Easy vector as directed in the kitmanual. (Promega, Madison, Wis.). The ligation mixture was added to 50μl of DH5a competent E. coli cells (Invitrogen, Carlsbad, Calif.) on icefor 2 minutes, incubated at 37° C. 5 minutes, incubated on ice for 2minutes, and then plated on LB+100 μg/L ampicillin agar plates andplaced at 37° C. for 14 hours. Individual bacterial colonies were pickedand placed in 5 ml of LB+100 μg/ampicillin and allowed to grow for 14hours. The tubes were spun down at 2000×g, 4° C. for 15 minutes and thevector DNA was prepared using Qiagen miniprep kit (Qiagen, Valencia,Calif.) as indicated in the kit manual. 2 μg of DNA was digested withAge I-Rsr-II. The fragment was gel purified by the Qiaquick method asinstructed in the kit manual (Qiagen, Valencia, Calif.) and ligated intopED.Epo Fc.1 Age I-Rsr II. The ligation was transformed into DH5acompetent E. coli cells and DNA prepped as described above.

Example 11 Cloning of Cvs-Fc Construct

Using PCR and standard molecular biology techniques (Sambrook et al.1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold SpringHarbor Laboratory Press), a mammalian expression construct was generatedsuch that the coding sequence for the human IFNα signal peptide wasdirectly abutted against the coding sequence of Fc beginning at thefirst cysteine residue (Cys 226, EU Numbering). Upon signal peptidasecleavage and secretion from mammalian cells, an Fc protein with anN-terminal cysteine residue was thus generated. Briefly, the primers

IFNa-Sig-F (IFNa-Sig-F: 5′-GCTACTGCAGCCACCATGGCCTTGACCTT TGCTTTAC-3′)(SEQ ID NO:71) and Cys-Fc-R (5′-CAGTTCCGGAGCTGGGCACGGCGGAGAGCCCACAGAGCAGCTTG-3′) (SEQ ID NO:72) were used in a PCR reaction tocreate a fragment linking the IFNα signal sequence with the N terminusof Fc, beginning with Cys 226. 500 ng of pED.dC.native hIFNα Δlinker wasadded to 25 pmol of each primer in a PCR reaction with Expand HighFidelity System (Boehringer Mannheim, Indianapolis, Ind.) according tomanufacturer's standard protocol. The reaction was carried out in a MJThermocycler using the following cycles: 94° C. 2 minutes; 30 cycles of(94° C. 30 seconds, 50° C. 30 seconds, 72° C. 45 seconds), and finally72° C. 10 minutes. The expected sized band (˜112 bp) was gel purifiedwith a Gel Extraction kit (Qiagen, Valencia Calif.), digested with thePstI and BspEI restriction enzymes, gel purified, and subcloned into thecorresponding sites pED.dC.native hIFNα Δlinker to generatepED.dC.Cys-Fc (FIG. 5).

Example 12 Protein Expression and Preparation of Fc-MESNA

The coding sequence for Fc (the constant region of human IgG1) wasobtained by PCR amplification from an Fc-containing plasmid usingstandard conditions and reagents, following the manufacturer'srecommended procedure to subclone the Fc coding sequence NdeI/SapI.Briefly, the primers 5′-GTGGTCATATGGGCATTGAAGGCAGAGGCGCCGCTGCGGTCG-3′(SEQ ID NO:73) and5′-GGTGGTTGCTCTTCCGCAAAAACCCGGAGACAGGGAGAGACTCTTCTGCG-3′ (SEQ ID NO:74)were used to amplify the Fc sequence from 500 ng of the plasmidpED.dC.Epo-Fc using Expand High Fidelity System (Boehringer Mannheim,Basel Switzerland) in a RapidCylcler thermocycler (Idaho Technology SaltLake City, Utah), denaturing at 95° C. for 2 minutes followed by 18cycles of 95° C. for 0 sec, 55° C. for 0 sec, and 72° C. for 1 minutewith a slope of 4, followed by 72° C. extension for 10 minutes. The PCRproduct was subcloned into an intermediate cloning vector and sequencedfully, and then subcloned using the NdeI and SapI sites in the pTVVIN1vector following standard procedures. Sambrook, J., Fritsch, E. F. andManiatis, T. 1989, Molecular Cloning: A Laboratory Manual, 2^(nd) ed.;Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press. Thisplasmid was then transformed into BL21(DE3) pLysS cells using standardmethods. Id. A 1 liter culture of cells was grown to an absorbancereading of 0.8 AU at 37° C., induced with 1 mM isopropylbeta-D-1-thiogalactopyranoside, and grown overnight at 25° C. Cells werepelleted by centrifugation, lysed in 20 mM Tris 8.8/r/o NP40/0.1 mMphenylmethanesulfonyl fluoride/1 μg/ml Benzonase (Novagen Madison,Wis.), and bound to chitin beads (New England Biolabs; Beverly, Mass.)overnight at 42° C. Beads were then washed with several column volumesof 20 mM Tris 8.5/500 mM NaCV 1 mM EDTA, and then stored at −80° C.Purified Fc-MESNA was generated by eluting the protein from the beads in20 mM Tris 8.5/500 mM NaCl/1 mM EDTA/500 mM 2-mercapto ethane sulfonicacid (MESNA), and the eluate was used directly in the coupling reaction,below.

Example 13 Factor VII-Fc Monomer-Dimer Hybrid Expression andPurification

CHO DG-44 cells expressing Factor VII-Fc were established. CHO DG-44cells were grown at 37° C., 5% CO₂, in MEM Alpha plus nucleoside andribonucleosides and supplemented with 5% heat-inactivated fetal bovineserum until transfection.

DG44 cells were plated in 100 mm tissue culture petri dishes and grownto a confluency of 50%-60%. A total of 10 μg of DNA was used totransfect one 100 mm dish: 7.5 μg of pED.dC.FVII-Fc+1.5 μgpcDNA3/Flag-Fc+1 μg of pcDNA6-PACE. The cells were transfected asdescribed in the Superfect transfection reagent manual (Qiagen,Valencia, Calif.). The media was removed from transfection after 48hours and replaced with MEM Alpha without nucleosides plus 5% dialyzedfetal bovine serum and 10 μg/ml of Blasticidin (Invitrogen, Carlsbad,Calif.) and 0.2 mg/ml geneticin (Invitrogen, Carlsbad, Calif.). After 10days, the cells were released from the plate with 0.25% trypsin andtransferred into T25 tissue culture flasks, and the selection wascontinued for 10-14 days until the cells began to grow well as stablecell lines were established. Protein expression was subsequentlyamplified by the addition 25 nM methotrexate.

Approximately 2×10⁷ cells were used to inoculate 300 ml of growth mediumin a 1700 cm2 roller bottle (Corning, Corning, N.Y.) supplemented with 5μg/ml of vitamin K3 (menadione sodium bisulfite) (Sigma, St Louis, Mo.).The roller bottles were incubated in a 5% CO₂ at 37° C. for 72 hours.Then the growth medium was exchanged with 300 nil serum-free productionmedium (DMEM/F12 with 5 μg/ml bovine insulin and 10 μg/ml Gentamicin)supplemented with 5 μg/L of vitamin K₃. The production medium(conditioned medium) was collected every day for 10 days and stored at4° C. Fresh production medium was added to the roller bottles after eachcollection and the bottles were returned to the incubator. Pooled mediawas first clarified using a Sartoclean glass fiber filter (3.0 μm+0.2μm) (Sartorious Corp. Gottingen, Germany) followed by an Acropack 500filter (0.8 μm+0.2 μm) (Pall Corp., East Hills, N.Y.). The clarifiedmedia was then concentrated approximately 20-fold using Pellicon Biomaxtangential flow filtration cassettes (10 kDa MWCO) (Millipore Corp.,Billerica, Mass.).

Fc chimeras were then captured from the concentrated media by passageover a Protein A Sepharose 4 Fast Flow Column (AP Biotech, Piscataway,N.J.). A 5×5 cm (100 ml) column was loaded with ≦5 mg Fc protein per mlcolumn volume at a linear flow rate of 100 cm/hour to achieve aresidence time of ≧3 minutes. The column was then washed with >5 columnvolumes of 1×DPBS to remove non-specifically bound proteins. The boundproteins were eluted with 100 mM Glycine pH 3.0. Elution fractionscontaining the protein peak were then neutralized by adding 1 part 1 MTris-HCL, pH 8 to 10 parts elute fraction.

To remove FLAG-Fc homodimers (that is, chimeric Fc dimers with FLAGpeptide expressed as fusions with both Fc molecules) from thepreparation, the Protein A Sepharose 4 Fast Flow pool was passed over aUnosphere S cation-exchange column (BioRad Corp., Richmond, Calif.).Under the operating conditions for the column, the FLAG-Fc monomer-dimerhybrid is uncharged (FLAG-Fc theoretical pI=6.19) and flows through thecolumn while the hFVII-Fc constructs are positively charged, and thusbind to the column and elute at higher ionic strength. The Protein ASepharose 4 Fast Flow pool was first dialyzed into 20 mM MES, 20 mMNaCl, pH 6.1. The dialyzed material was then loaded onto a 1.1×11 cm(9.9 ml) column at 150 cm/hour. During the wash and elution, the flowrate was increased to 500 cm/hour. The column was washed sequentiallywith 8 column volumes of 20 mM MES, 20 mM NaCl, pH 6.1 and 8 columnvolumes of 20 mM MES, 40 mM NaCl, pH 6.1. The bound protein was elutedwith 20 mM MES, 750 mM NaCl, pH 6.1. Elution fractions containing theprotein peak were pooled and sterile filtered through a 0.2 μm filterdisc prior to storage at −80° C.

An anti-FLAG MAB affinity column was used to separate chimeric Fc dimerswith hFVII fused to both Fc molecules from those with one FLAG peptideand one hFVII fusion. The Unosphere S Eluate pool was diluted 1:1 with20 mM Tris, 50 mM NaCl, 5 mM CaCl₂, pH 8 and loaded onto a 1.6×5 cm M2anti-FLAG sepharose column (Sigma Corp., St. Louis, Mo.) at a linearflow rate of 60 cm/hour. Loading was targeted to <2.5 mg monomer-dimerhybrid/ml column volume. After loading the column was washed with 5column volumes 20 mM Tris, 50 mM NaCl, 5 mM CaCl₂, pH 8.0, monomer-dimerhybrids were then eluted with 100 mM Glycine, pH 3.0. Elution fractionscontaining the protein peak were then neutralized by adding 1 part 1 MTris-HCl, pH 8 to 10 parts eluate fraction. Pools were stored at −80° C.

Example 14 Factor IX-Fc Homodimer and Monomer-Dimer Hybrid Expressionand Purification

CHO DG-44 cells expressing Factor IX-Fc were established. DG44 cellswere plated in 100 mm tissue culture petri dishes and grown to aconfluency of 50%-60%. A total of 10 μg of DNA was used to transfect one100 mm dish: for the homodimer transfection, 8 μg of pED.dC.FactorIX-Fc+2 μg of pcDNA6-PACE was used; for the monomer-dimer hybridtransfection, 8 μg of pED.dC.Factor IX-Fc+1 μg of pcDNA3-FlagFc+1 μgpcDNA6-PACE was used. The cells were transfected as described in theSuperfect transfection reagent manual (Qiagen, Valencia, Calif.). Themedia was removed from transfection after 48 hours and replaced with MEMAlpha without nucleosides plus 5% dialyzed fetal bovine serum and 10μg/ml of Blasticidin (Invitrogen, Carlsbad, Calif.) for bothtransfections, while the monomer-dimer hybrid transfection was alsosupplemented with 0.2 mg/ml geneticin (Invitrogen, Carlsbad, Calif.).After 3 days, the cells were released from the plate with 0.25% trypsinand transferred into T25 tissue culture flasks, and the selection wascontinued for 10-14 days until the cells began to grow well as stablecell lines were established. Protein expression was subsequentlyamplified by the addition 10 nM or 100 nM methotrexate for the homodimeror monomer-dimer hybrid, respectively.

For both cell lines, approximately 2×10⁷ cells were used to inoculate300 ml of growth medium in a 1700 cm² roller bottle (Corning, Corning,N.Y.), supplemented with 5 μg/L of vitamin K₃ (menadione sodiumbisulfite) (Sigma, St. Louis, Mo.). The roller bottles were incubated ina 5% CO₂ at 37° C. for approximately 72 hours. The growth medium wasexchanged with 300 ml serum-free production medium (DMEM/F12 with 5μg/ml bovine insulin and 10 μg/ml Gentamicin), supplemented with 5 μg/ofvitamin K₃. The production medium (conditioned medium) was collectedeveryday for 10 days and stored at 4° C. Fresh production medium wasadded to the roller bottles after each collection and the bottles werereturned to the incubator. Prior to chromatography, the medium wasclarified using a Supor Cap-100 (0.8/0.2 μm) filter (Pall GelmanSciences, Ann Arbor, Mich.). All of the following steps were performedat 4° C. The clarified medium was applied to Protein A Sepharose, washedwith 5 column volumes of 1×PBS (10 mM phosphate, pH 7.4, 2.7 mM KCl, and137 mM NaCl), eluted with 0.1 M glycine, pH 2.7, and then neutralizedwith 1/10 volume of 1 M Tris-HCl, pH 9.0. The protein was then dialyzedinto PBS.

The monomer-dimer hybrid transfection protein sample was subject tofurther purification, as it contained a mixture of FIX-Fc:FIX-Fchomodimer, FIX-Fc:Flag-Fc monomer-dimer hybrid, and Flag-Fc:Flag-Fchomodimer. Material was concentrated and applied to a 2.6 cm×60 cm (318ml) Superdex 200 Prep Grade column at a flow rate of 4 ml/minute (36cm/hour) and then eluted with 3 column volumes of 1×PBS. Fractionscorresponding to two peaks on the UV detector were collected andanalyzed by SDS-PAGE. Fractions from the first peak contained eitherFIX-Fc:FIX-Fc homodimer or FIX-Fc:FlagFc monomer-dimer hybrid, while thesecond peak contained FlagFc:FlagFc homodimer. All fractions containingthe monomer-dimer hybrid but no FlagFc homodimer were pooled and applieddirectly to a 1.6×5 cm M2 anti-FLAG sepharose column (Sigma Corp., St.Louis, Mo.) at a linear flow rate of 60 cm/hour. After loading, thecolumn was washed with 5 column volumes PBS. Monomer-dimer hybrids werethen eluted with 100 mM Glycine, pH 3.0. Elution fractions containingthe protein peak were then neutralized by adding 1/10 volume of 1 MTris-HCl, and analyzed by reducing and nonreducing SDS-PAGE. Fractionswere dialyzed into PBS, concentrated to 1-5 mg/ml, and stored at −80° C.

Example 15 IFNα Homodimer and Monomer-Dimer Hybrid Expression andPurification

CHO DG-44 cells expressing hIFNα were established. DG44 cells wereplated in 100 mm tissue culture petri dishes and grown to a confluencyof 50%-60%. A total of 10 μg of DNA was used to transfect one 100 mmdish: for the homodimer transfection, 10 μg of the hIFNαFc constructs;for the monomer-dimer hybrid transfection, 8 μg of the hIFNαFcconstructs+2 μg of pcDNA3-FlagFc. The cells were transfected asdescribed in the Superfect transfection reagent manual (Qiagen,Valencia, Calif.). The media was removed from transfection after 48hours and replaced with MEM Alpha without nucleosides plus 5% dialyzedfetal bovine serum, while the monomer-dimer hybrid transfection was alsosupplemented with 0.2 mg/ml geneticin (Invitrogen, Carlsbad, Calif.).After 3 days, the cells were released from the plate with 0.25% trypsinand transferred into T25 tissue culture flasks, and the selection wascontinued for 10-14 days until the cells began to grow well and stablecell lines were established. Protein expression was subsequentlyamplified by the addition methotrexate: ranging from 10 to 50 nM.

For all cell lines, approximately 2×10⁷ cells were used to inoculate 300ml of growth medium in a 1700 cm² roller bottle (Corning, Corning,N.Y.). The roller bottles were incubated in a 5% CO₂ at 372 C forapproximately 72 hours. Then the growth medium was exchanged with 300 mlserum-free production medium (DMEM/F12 with 5 μg/ml bovine insulin and10 μg/ml Gentamicin). The production medium (conditioned medium) wascollected every day for 10 days and stored at 4° C. Fresh productionmedium was added to the roller bottles after each collection and thebottles were returned to the incubator. Prior to chromatography, themedium was clarified using a Supor Cap-100 (0.8/0.2 μm) filter from PallGelman Sciences (Ann Arbor, Mich.). All of the following steps wereperformed at 4° C. The clarified medium was applied to Protein ASepharose, washed with 5 column volumes of 1×PBS (10 mM phosphate, pH7.4, 2.7 mM KCl, and 137 mM NaCl), eluted with 0.1 M glycine, pH 2.7,and then neutralized with 1/10 volume of 1 M Tris-HCl, pH 9.0. Theprotein was then dialyzed into PBS.

The monomer-dimer hybrid transfection protein samples were then subjectto further purification, as it contained a mixture of IFNαFc:IFNαFchomodimer, IFNαFc:FlagFc monomer-dimer hybrid, and FlagFc:FlagFchomodimer (or Δlinker or GS15 linker). Material was concentrated andapplied to a 2.6 cm×60 cm (318 ml) Superdex 200 Prep Grade column at aflow rate of 4 ml/min (36 cm/hr) and then eluted with 3 column volumesof 1×PBS. Fractions corresponding to two peaks on the UV detector werecollected and analyzed by SDS-PAGE. Fractions from the first peakcontained either IFNαFc:IFNαFc homodimer or IFNαFc:FlagFc monomer-dimerhybrid, while the second peak contained FlagFc:FlagFc homodimer. Allfractions containing the monomer-dimer hybrid, but no FlagFc homodimer,were pooled and applied directly to a 1.6×5 cm M2 anti-FLAG sepharosecolumn (Sigma Corp., St. Louis, Mo.) at a linear flow rate of 60cm/hour. After loading the column was washed with 5 column volumes PBSmonomer-dimer hybrids were then eluted with 100 mM Glycine, pH 3.0.Elution fractions containing the protein peak were then neutralized byadding 1/10 volume of 1 M Tris-HCl, and analyzed by reducing andnonreducing SDS-PAGE. Fractions were dialyzed into PBS, concentrated to1-5 mg/ml, and stored at −80° C.

Example 16 Coiled Coil Protein Expression and Purification

The plasmids, pED.dC Epo-CCA-Fc and pED.dC CCB-Fc will be transfectedeither alone or together at a 1:1 ratio into CHO DG44 cells. The cellswill be transfected as described in the Superfect transfection reagentmanual (Qiagen, Valencia, Calif.). The media will be removed after 48hours and replaced with MEM Alpha w/o nucleosides plus 5% dialyzed fetalbovine serum. Purification will be done by affinity chromatography overa protein A column according to methods known in the art. Alternatively,purification can be achieved using size exclusion chromatography.

Example 17 Cvs-Fc Expression and Purification

CHO DG-44 cells expressing Cys-Fc were established. The pED.dC.Cys-Fcexpression plasmid, which contains the mouse dihydrofolate reductase(dhfr) gene, was transfected into CHO DG44 (dhfr deficient) cells usingSuperfect reagent (Qiagen; Valencia, Calif.) according to manufacturer'sprotocol, followed by selection for stable transfectants in aMEM(without nucleosides) tissue culture media supplemented with 5% dialyzedFBS and penicillin/streptomycin antibiotics (Invitrogen; Carlsbad,Calif.) for 10 days. The resulting pool of stably transfected cells werethen amplified with 50 nM methotrexate to increase expression.Approximately 2×10⁷ cells were used to inoculate 300 ml of growth mediumin a 1700 cm² roller bottle (Corning, Corning, N.Y.). The roller bottleswere incubated in a 5% CO₂ at 37⁻⁹-C for approximately 72 hours. Thegrowth medium was exchanged with 300 nil serum-free production medium(DMEIV1/F12 with 5 μg/ml bovine insulin and 10 μg/ml Gentamicin). Theproduction medium (conditioned medium) was collected every day for 10days and stored at 4° C. Fresh production medium was added to the rollerbottles after each collection and the bottles were returned to theincubator. Prior to chromatography, the medium was clarified using aSupor Cap-100 (0.8/0.2 μm) filter from Pall Gelman Sciences (Ann Arbor,Mich.). All of the following steps were performed at 4° C. The clarifiedmedium was applied to Protein A Sepharose, washed with 5 column volumesof lx PBS (10 mM phosphate, pH 7.4, 2.7 mM KCl, and 137 mM NaCl), elutedwith 0.1 M glycine, pH 2.7, and then neutralized with 1/10 volume of 1 MTris-HCl, pH 9.0. Protein was dialyzed into PBS and used directly inconjugation reactions.

Example 18 Coupling of T20-Thioesters to Cvs-Fc

Cys-Fc (4 mg, 3.2 mg/ml final concentration) and either T20-thioester orT20-PEG-thioester (2 mg, approximately 5 molar equivalents) wereincubated for 16 hours at room temperature in 0.1 M Tris 8/10 mM MESNA.Analysis by SDS-PAGE (Tris-Gly gel) using reducing sample bufferindicated the presence of a new band approximately 5 kDa larger than theFc control (>40-50% conversion to the conjugate). Previous N-terminalsequencing of Cys-Fc and unreacted Cys-Fc indicated that the signalpeptide is incorrectly processed in a fraction of the molecules, leavinga mixture of (Cys)-Fc, which will react through native ligation withpeptide-thioesters, and (Val)-(Gly)-(Cys)-Fc, which will not. As thereaction conditions are insufficient to disrupt the dimerization of theCys-Fc molecules, this reaction generated a mixture ofT20-Cys-Fc:T20-Cys-Fc homodimers, T20-Cys-Fc: Fc monomer-dimer hybrids,and Cys-Fc:Cys-Fc Fc-dimers. This protein was purified using sizeexclusion chromatography as indicated above to separate the threespecies. The result was confirmed by SDS-PAGE analysis under nonreducingconditions.

Example 19 Antiviral Assay for IFNα Activity

Antiviral activity (IU/ml) of IFNα fusion proteins was determined usinga CPE (cytopathic effect) assay. A549 cells were plated in a 96 welltissue culture plate in growth media (RPMI 1640 supplemented with 10%fetal bovine serum (FBS) and 2 mM L-glutamine) for 2 hours at 37° C., 5%CO₂. IFNα standards and IFNα fusion proteins were diluted in growthmedia and added to cells in triplicate for 20 hours at 37° C., 5% CO₂.Following incubation, all media was removed from wells,encephalomyocarditis virus (EMC) virus was diluted in growth media andadded (3000 pfu/well) to each well with the exception of control wells.Plates were incubated at 37° C., 5% CO₂ for 28 hours. Living cells werefixed with 10% cold trichloroacetic acid (TCA) and then stained withSulforhodamine B (SRB) according to published protocols (Rubinstein etal. 1990, J. Natl. Cancer Inst. 82, 1113). The SRB dye was solubilizedwith 10 mM Tris pH 10.5 and read on a spectrophotometer at 490 nm.Samples were analyzed by comparing activities to a known standard curveWorld Health Organization IFNα 2b International Standard ranging from 5to 0.011 IU/ml. The results are presented below in Table 3 and FIG. 6and demonstrate increased antiviral activity of monomer-dimer hybrids.

TABLE 3 INTERFERON ANTIVIRAL ASSAY HOMODIMER V. MONOMER-DIMER HYBRIDAntiviral Activity Protein (IU/nmol) Std dev IFNaFc 8aa linker homodimer0.45 × 10⁵   0.29 × 10⁵ IFNaFc 8aa linker: FlagFc  4.5 × 10⁵    1.2 ×10⁵ monomer-dimer hybrid IFNαFc Δ linker homodimer 0.22 × 10⁵   0.07 ×10⁵ IFNαFc Δ delta linker: FlagFc  2.4 × 10⁵ 0.0005 × 10⁵ monomer-dimerhybrid IFNαFc GS15 linker  2.3 × 10⁵    1.0 × 10⁵ homodimer IFNαFc GS15linker  5.3 × 10⁵   0.15 × 10⁵ monomer-dimer hybrid

Example 20 FVIIa Clotting Activity Analysis

The StaClot FVIIa-rTF assay kit was purchased from Diagnostica Stago(Parsippany, N.J.) and modified as described in Johannessen et al. 2000,Blood Coagulation and Fibrinolysis 11:S159. A standard curve waspreformed with the FVIIa World Health Organization standard 89/688. Theassay was used to compare clotting activity of monomer-dimer hybridscompared to homodimers. The results showed the monomer-dimer hybrid hadfour times the clotting activity compared to the homodimer (FIG. 7).

Example 21 FVIIa-Fc Oral Dosing in Day 10 Rats

25 gram day 9 newborn Sprague Dawley rats were purchased from CharlesRiver (Wilmington, Mass.) and allowed to acclimate for 24 hours. Therats were dosed orally with FVIIaFc homodimer, monomer-dimer hybrid or a50:50 mix of the two. A volume of 200 μl of a FVIIaFc solution for adose of 1 mg/kg was administered. The solution was composed of aTris-HCl buffer pH 7.4 with 5 mg/ml soybean trypsin inhibitor. The ratswere euthanized with CO₂ at several time points, and 200 μl of blood wasdrawn by cardiac puncture. Plasma was obtained by the addition of a 3.8%sodium citrate solution and centrifugation at mom temperature at a speedof 1268×g. The plasma samples were either assayed fresh or frozen at 20°C. Orally dosed monomer-dimer hybrid resulted in significantly highermaximum (C_(max)) serum concentrations compared to homodimeric FactorVII (FIG. 8).

Example 22 Factor IX-Fc Oral Closing of Neonatal Rats

Ten-day old neonatal Sprague-Dawley rats were dosed p.o. with 200 μl ofFIX-Fc homodimer or FIX-Fc: FlagFc monomer-dimer hybrid at approximatelyequimolar doses of 10 nmol/kg in 0.1 M sodium phosphate buffer, pH 6.5containing 5 mg/ml soybean trypsin inhibitor and 0.9% NaCl. At 1, 2, 4,8, 24, 48, and 72 hours post injection, animals were euthanized withCO₂, blood was drawn via cardiac puncture and plasma was obtained by theaddition of a 3.8% sodium citrate solution and centrifugation at roomtemperature at a speed of 1268×g. Samples were then sedimented bycentrifugation, serum collected and frozen at −20° C. until analysis ofthe fusion proteins by ELISA.

Example 23 Factor IX-Fc ELISA

A 96-well lmmulon 4HBX ELISA plate (Thermo LabSystems, Vantaa, Finland)was coated with 100 μl/well of goat anti-Factor IX IgG (AffinityBiologicals, Ancaster, Canada) diluted 1:100 in 50 mM carbonate buffer,pH 9.6. The plates were incubated at ambient temperature for 2 hours orovernight at 4° C. sealed with plastic film. The wells were washed 4times with PBST, 300 μl/well using the TECAN plate washer. The wellswere blocked with PBST+6% BSA, 200 μl/well, and incubated 90 minutes atambient temperature. The wells were washed 4 times with PBST, 300μl/well using the TECAN plate washer. Standards and blood samples fromrats described in Example 18 were added to the wells, (100 μl/well), andincubated 90 minutes at ambient temperature. Samples and standards werediluted in HBET buffer (HBET: 5.95 g HEPES, 1.46 g NaCl, 0.93 g Na₂EDTA,2.5 g Bovine Serum Albumin, 0.25 ml Tween-20, bring up to 250 ml withdH₂O, adjust pH to 7.2). Standard curve range was from 200 ng/ml to 0.78ng/ml with 2 fold dilutions in between. Wells were washed 4 times withPBST, 300 μl/well using the TECAN plate washer. 100 μl/well ofconjugated goat anti-human IgG-Fc-HARP antibody (Pierce, Rockford, Ill.)diluted in HBET 1:25,000 was added to each well. The plates wereincubated 90 minutes at ambient temperature. The wells were washed 4times with PBST, 300 μl/well using the TECAN plate washer. The plateswere developed with 100 μl/well of tetramethylbenzidine peroxidasesubstrate (TMB) (Pierce, Rockford, Ill.) was added according to themanufacturer's instructions. The plates were incubated 5 minutes atambient temperature in the dark or until color developed. The reactionwas stopped with 100 μl/well of 2 M sulfuric acid. Absorbance was readat 450 nm on SpectraMax plusplate reader (Molecular Devices, Sunnyvale,Calif.). Analysis of blood drawn at 4 hours indicated more than a 10fold difference in serum concentration between Factor IX-Fcmonomer-dimer hybrids compared to Factor IX Fc homodimers (FIG. 9). Theresults indicated Factor IX-Fc monomer-dimer hybrid levels wereconsistently higher than Factor IX-Fc homodimers (FIG. 10).

Example 24 Cloning of Epo-Fc

The mature Epo coding region was obtained by PCR amplification from aplasmid encoding the mature erythropoietin coding sequence, originallyobtained by RT-PCR from Hep G2 mRNA, and primers hepoxba-F andhepoeco-R, indicated below. Primer hepoxba-F contains an XbaI site,while primer hepoeco-R contains an EcoRI site. PCR was carried out inthe Idaho Technology RapidCycler using Vent polymerase, denaturing at95° C. for 15 seconds, followed by 28 cycles with a slope of 6.0 of 95°C. for 0 seconds, 55° C. for 0 seconds, and 72° C. for 1 minute 20seconds, followed by 3 minute extension at 72° C. An approximately 514bp product was gel purified, digested with XbaI and EcoRI, gel purifiedagain and directionally subcloned into an XbaI/EcoRI-digested, gelpurified pED.dC.XFc vector, mentioned above. This construct was namedpED.dC.EpoFc.

The Epo sequence, containing both the endogenous signal peptide and themature sequence, was obtained by PCR amplification using an adult kidneyQUICK-clone cDNA preparation as the template and primers Epo+Pep-Sbf-Fand Epo+Pep-Sbf-R, described below. The primer Epo+Pep-Sbf-F contains anSbfI site upstream of the start codon, while the primer Epo+Pep-Sbf-Ranneals downstream of the endogenous SbfI site in the Epo sequence. ThePCR reaction was carried out in the PTC-200 MJ Thermocycler using Expandpolymerase, denaturing at 94° C. for 2 minutes, followed by 32 cycles of94° C. for 30 seconds, 57° C. for 30 seconds, and 72° C. for 45 seconds,followed by a 10 minute extension at 72° C. An approximately 603 bpproduct was gel isolated and subcloned into the pGEM-T Easy vector. Thecorrect coding sequence was excised by WI digestion, gel purified, andcloned into the PstI-digested, shrimp alkaline phosphatase(SAP)-treated, gel purified pED.dC.EpoFc plasmid. The plasmid with theinsert in the correct orientation was initially determined by KpnIdigestion. A XmnI and PvuII digestion of this construct was comparedwith pED.dC.EpoFc and confirmed to be in the correct orientation. Thesequence was determined and the construct was named pED.dC.natEpoFc. PCRPrimers:

hepoxba-F (EPO-F): (SEQ ID NO: 75)5′-AATCTAGAGCCCCACCACGCCTCATCTGTGAC-3′ hepoeco-R (EPO-R) (SEQ ID NO: 76)5′-TTGAATTCTCTGTCCCCTGTCCTGCAGGCC-3′ Epo + Pep-Sbf-F: (SEQ ID NO: 77)5′-GTACCTGCAGGCGGAGATGGGGGTGCA-3′ Epo + Pep-Sbf-R: (SEQ ID NO: 78)5′-CCTGGTCATCTGTCCCCTGICC-3′

Example 25 Cloning of Epo-Fc

An alternative method of cloning EPO-Fc is described herein. Primerswere first designed to amplify the full length Epo coding sequence,including the native signal sequence, as follows:

Epo-F: (SEQ ID NO: 79) 5′-GTCCAACCTG CAGGAAGCTTG CCGCCACCAT GGGAGTGCACGAATGTCCTG CCTGG- 3′ Epo-R: (SEQ ID NO: 80)5′-GCCGAATTCA GTTTTGTCGA CCGCAGCGG CGCCGGCGAACTCTCTGTCC CCTGTTCTGC AGGCCTCC- 3′

The forward primer incorporates an SbfI and HindIII site upstream of aKozak sequence, while the reverse primer removes the internal SbfI site,and adds an 8 amino acid linker to the 3′ end of the coding sequence(EFAGAAAV) (SEQ ID NO: 31) as well as SalI and EcoRI restriction sites.The Epo coding sequence was then amplified from a kidney cDNA library(BD Biosciences Clontech, Palo Alto, Calif.) using 25 pmol of theseprimers in a 25 μl PCR reaction using Expand High Fidelity System(Boehringer Mannheim, Indianapolis, Ind.) according to manufacturer'sstandard protocol in a MJ Thermocycler using the following cycles: 94°C. 2 minutes; 30 cycles of (94° C. 30 seconds, 58° C. 30 seconds, 72° C.45 seconds), followed by 72° C. for 10 minutes. The expected sized band(641 bp) was gel purified with a Gel Extraction kit (Qiagen, Valencia,Calif.) and ligated into the intermediate cloning vector pGEM T-Easy(Promega, Madison, Wis.). DNA was transformed into DH5a cells(Invitrogen, Carlsbad, Calif.) and miniprep cultures grown and purifiedwith a Plasmid Miniprep Kit (Qiagen, Valencia, Calif.) both according tomanufacturer's standard protocols. Once the sequence was confirmed, thisinsert was digested out with SbfI/EcoRI restriction enzymes, gelpurified, and cloned into the PstI/EcoRI sites of the mammalianexpression vector pED.dC in a similar manner.

Primers were designed to amplify the coding sequence for the constantregion of human IgG1 (the Fc region, EU numbering 221-447) as follows:

Fc-F: (SEQ ID NO: 82) 5′-GCTGCGGTCG ACAAAACTCA CACATGCCCA CCGTGCCCAGCTCCGGAACT CCTGGGCGGA CCGTCAGTC- 3′ Fc-R (SEQ ID NO: 83)5′-ATTGGAATTC TCATTTACCC GGAGACAGGG AGAGGC- 3′The forward primer incorporates a SalI site at the linker-Fc junction,as well as introducing BspEI and RsrII sites into the Fc region withoutaffecting the coding sequence, while the reverse primer adds an EcoRIsite after the stop codon. The Fc coding sequence was then amplifiedfrom a leukocyte cDNA library (BD Biosciences Clontech, Palo Alto,Calif.) using 25 pmol of these primers in a 25 μl PCR reaction usingExpand High Fidelity System (Boehringer Mannheim, Indianapolis, Ind.)according to manufacturer's standard protocol in a MJ Thermocycler usingthe following cycles: 94° C. 2 minutes; 30 cycles of (94° C. 30 seconds,58° C. 30 seconds, 72° C. 45 seconds), followed by 72° C. for 10minutes. The expected sized band (696 bp) was gel purified with a GelExtraction kit (Qiagen, Valencia, Calif.) and ligated into theintermediate cloning vector pGEM T-Easy (Promega, Madison, Wis.). DNAwas transformed into DH5a cells (Invitrogen, Carlsbad, Calif.) andminiprep cultures grown and purified with a Plasmid Miniprep Kit(Qiagen, Valencia, Calif.), both according to manufacturer's standardprotocols. Once the sequence was confirmed, this insert was digested outwith Sal/EcoRI restriction enzymes, gel purified, and cloned into theSalI/EcoRI sites of the plasmid pED.dC.Epo (above) in a similar manner,to generate the mammalian expression plasmid pED.dC.EpoFc. In anotherexperiment this plasmid was also digested with RsrII/Xmal, and thecorresponding fragment from pSYN-Fc-002, which contains the Asn 297 Alamutation (EU numbering) was cloned in to create pED.dC.EPO-Fc N297A(pSYN-EPO-004). Expression in mammalian cells was as described inExample 26. The amino acid sequence of EpoFc with an eight amino acidlinker is provided in FIG. 2 j. During the process of this alternativecloning method, although the exact EpoFc amino acid sequence waspreserved (FIG. 2J), a number of non-coding changes were made at thenucleotide level (FIG. 3J). These are G6A (G at nucleotide 6 changed toA) (eliminate possible secondary structure in primer), G567A (removesendogenous SbfI site from Epo), A582G (removes EcoRI site from linker),A636T and T639G (adds unique BspEI site to Fc), and G651C (adds uniqueRsrII site to Fc). The nucleotide sequence in FIG. 3J is from theconstruct made in Example 25, which incorporates these differences fromthe sequence of the construct from Example 24.

Example 26 EPO-Fc Homodimer and Monomer-Dimer Hybrid Expression andPurification

DG44 cells were plated in 100 mm tissue culture petri dishes and grownto a confluency of 50%-60%. A total of 10 μg of DNA was used totransfect one 100 mm dish: for the homodimer transfection, 10 μg ofpED.dC.EPO-Fc; for the monomer-dimer hybrid transfection, 8 μg ofpED.dC.EPO-Fc+2 μg of pcDNA3-FlagFc. The constructs used were cloned asdescribed in Example 24. The cloning method described in Example 25could also be used to obtain constructs for use in this example. Thecells were transfected as described in the Superfect transfectionreagent manual (Qiagen, Valencia, Calif.). Alternatively, pED.dC.EPO-Fcwas cotransfected with pSYN-Fc-016 to make an untagged monomer. Themedia was removed from transfection after 48 hours and replaced with MEMAlpha without nucleosides plus 5% dialyzed fetal bovine serum for bothtransfections, while the monomer-dimer hybrid transfection was alsosupplemented with 0.2 mg/ml geneticin (Invitrogen, Carlsbad, Calif.).After 3 days, the cells were released from the plate with 0.25% trypsinand transferred into T25 tissue culture flasks, and the selection wascontinued for 10-14 days until the cells began to grow well as stablecell lines were established. Protein expression was subsequentlyamplified by the addition methotrexate.

For both cell lines, approximately 2×10⁷ cells were used to inoculate300 ml of growth medium in a 1700 cm² roller bottle (Corning, Corning,N.Y.). The roller bottles were incubated in a 5% CO₂ at 37° C. forapproximately 72 hours. The growth medium was exchanged with 300 mlserum-free production medium (DMEM/F12 with 5 μg/mlbovine insulin and 10μg/mlGentamicin). The production medium (conditioned medium) wascollected every day for 10 days and stored at 4° C. Fresh productionmedium was added to the roller bottles after each collection and thebottles were returned to the incubator. Prior to chromatography, themedium was clarified using a Supor Cap-100 (0.8/0.2 μm) filter from PallGelman Sciences (Ann Arbor, Mich.). All of the following steps wereperformed at 4° C. The clarified medium was applied to Protein ASepharose, washed with 5 column volumes of 1×PBS (10 mM phosphate, pH7.4, 2.7 mM KCl, and 137 mM NaCl), eluted with 0.1 M glycine, pH 2.7,and then neutralized with 1/10 volume of 1 M Tris-HCl, pH 9.0. Proteinwas then dialyzed into PBS.

The monomer-dimer hybrid transfection protein sample was subject tofurther purification, as it contained a mixture of EPO-Fc:EPO-Fchomodimer, EPO-Fc:Flag-Fc monomer-dimer hybrid, and Flag-Fc:Flag-Fchomodimer. Material was concentrated and applied to a 2.6 cm×60 cm (318ml) Superdex 200 Prep Grade column at a flow rate of 4 ml/min (36cm/hour) and then eluted with 3 column volumes of 1×PBS. Fractionscorresponding to two peaks on the UV detector were collected andanalyzed by SDS-PAGE. Fractions from the first peak contained eitherEPO-Fc:EPO-Fc homodimer or EPO-Fc:FlagFc monomer-dimer hybrid, while thesecond peak contained FlagFc:FlagFc homodimer. All fractions containingthe monomer-dinner hybrid but no FlagFc homodimer were pooled andapplied directly to a 1.6×5 cm M2 anti-FLAG sepharose column (SigmaCorp.) at a linear flow rate of 60 cm/hour. After loading the column waswashed with 5 column volumes PBS. Monomer-dimer hybrids were then elutedwith 100 mM Glycine, pH 3.0. Elution fractions containing the proteinpeak were then neutralized by adding 1/10 volume of 1 M Tris-HCl, andanalyzed by reducing and nonreducing SDS-PAGE. Fractions were dialyzedinto PBS, concentrated to 1-5 mg/ml, and stored at −80° C.

Alternatively, fractions from first peak of the Superdex 200 wereanalyzed by SDS-PAGE, and only fractions containing a majority of EpoFcmonomer-dimer hybrid, with a minority of EpoFc homodimer, were pooled.This pool, enriched for the monomer-dimer hybrid, was then reapplied toa Superdex 200 column, and fractions containing only EpoFc monomer-dimerhybrid were then pooled, dialyzed and stored as purified protein. Notethat this alternate purification method could be used to purifynon-tagged monomer-dimer hybrids as well.

Example 27 Administration of EpoFc Dimer and Monomer-Dimer Hybrid withan Eight Amino Acid Linker to Cynomolgus Monkeys

For pulmonary administration, aerosols of either EpoFc dimer or EpoFcmonomer-dimer hybrid proteins (both with the 8 amino acid linker) inPBS, pH 7.4 were created with the Aeroneb Pro™ (AeroGen, Mountain View,Calif.) nebulizer, in-line with a Bird Mark 7A respirator, andadministered to anesthetized naïve cynomolgus monkeys throughendotracheal tubes (approximating normal tidal breathing). Both proteinswere also administered to naIve cynomolgus monkeys by intravenousinjection. Samples were taken at various time points, and the amount ofEpo-containing protein in the resulting plasma was quantitated using theQuantikine IVD Human Epo Immunoassay (R&D Systems, Minneapolis, Minn.).Pharmacokinetic parameters were calculated using the software WinNonLin.Table 4 presents the bioavailability results of cynomolgus monkeystreated with EpoFc monomer-dimer hybrid or EpoFc dimer.

TABLE 4 ADMINISTRATION OF EPOFC MONOMER-DIMER HYBRID AND EPOFC DIMER TOMONKEYS Approx. Deposited Cmax Cmax Monkey Dose¹ (ng/ (fmol/ t_(1/2)t_(1/2) avg Protein # Route (μg/kg) ml) ml) (hr) (hr) EpoFc C06181 pulm20 72.3 1014 23.6 25.2 mono- C06214 pulm 20 50.1 703 23.5 mer- C07300pulm 20 120 1684 36.2 dimer C07332 pulm 20 100 1403 17.5 hybrid C07285IV 25 749 10508 21.3 22.6 C07288 IV 25 566 7941 23 C07343 IV 25 551 101423.5 EpoFc DD026 pulm 15 10.7 120 11.5 22.1 dimer DD062 pulm 15 21.8 24427.3 DD046 pulm 15 6.4 72 21.8 DD015 pulm 15 12.8 143 20.9 DD038 pulm 3527 302 29 F4921 IV 150 3701 41454 15.1 14.6 96Z002 IV 150 3680 4121915.3 1261CQ IV 150 2726 30533 23.6 127-107 IV 150 4230 47379 15.0 118-22IV 150 4500 50403 8.7 126-60 IV 150 3531 39550 9.8 ¹Based on 15%deposition fraction or nebulized dose as determined by gammascintigraphy

The percent bioavailability (F) was calculated for the pulmonary dosesusing the following equation:

F=(AUC pulmonary/Dose pulmonary)/(AUC IV/Dose IV)*100

TABLE 5 CALCULATION OF PERCENT BIOAVAILABILITY FOR EPOFC MONOMER-DIMERHYBRID V. DIMER AFTER PULMONARY ADMINISTRATION TO NAIVE CYNOMOLGUSMONKEYS Approx. Bioavail- Average Dose¹ AUC ability² Bioavail- ProteinMonkey # (deposited) ng · hr/mL (F) abiity EpoFc C06181 20 μg/kg 381025.2% 34.9% monomer- C06214 20 μg/kg 3072 20.3% dimer C07300 20 μg/kg9525 63.0% hybrid C07332 20 μg/kg 4708 31.1% EpoFc DD026 15 μg/kg 361 5.1% 10.0% dimer DD062 15 μg/kg 1392 19.6% DD046 15 μg/kg 267  3.8%DD015 15 μg/kg 647  9.1% DD038 35 μg/kg 2062 12.4% ¹Based on 15%deposition fraction of nebulized dose as determined by gammascintigraphy ²Mean AUC for IV EpoFc monomer-dimer hybrid = 18,913 ng ·hr/mL (n = 3 monkeys), dosed at 25 μg/kg. Mean AUC for IV EpoFc dimer =70,967 ng · hr/mL (n = 6 monkeys), dosed at 150 μg/kg

The pharmacokinetics of EpoFc with an 8 amino acid linker administeredto cynomolgus monkeys is presented in FIG. 11. The figure compares theEpoFc dimer with the EpoFc monomer-dimer hybrid in monkeys afteradministration of a single pulmonary dose. Based on a molar comparisonsignificantly higher serum levels were obtained in monkeys treated withthe monomer-dimer hybrid compared to the dimer.

Example 28 Subcutaneous Administration of EPOFc Monomer-Dimer Hybrid

To compare serum concentrations of known erythropoietin agents withEPOFc monomer-dimer hybrids, both EPOFc monomer-dimer hybrid andAranesp® (darbepoetin alfa), which is not a chimeric fusion protein,were administered subcutaneously to different monkeys and the serumconcentration of both was measured over time.

Cynomolgus monkeys (n=3 per group) were injected subcutaneously with0.025 mg/kg EpoFc monomer-dimer hybrid. Blood samples were collectedpredose and at times up to 144 hours post dose. Serum was prepared fromthe blood and stored frozen until analysis by ELISA (Human EpoQuantikine Immunoassay) (R & D Systems, Minneapolis, Minn.).Pharmacokinetic parameters were determined using WinNonLinâ® software(Pharsight, Mountainview, Calif.).

The results indicated the serum concentrations of both EPOFcmonomer-dimer hybrid and Aranesp® (darbepoetin alfa) were equivalentover time, even though the administered molar dose of Aranesp®(darbepoetin alfa) was slightly larger (Table 6) (FIG. 12).

TABLE 6 % Dose Dose Cmax AUC T_(1/2) Bioavailability Route (μg/kg)(nmol/kg) (ng/mL) (ng · hr · mL⁻¹) (hr) (F) EpoFc Subcutaneous 25 0.3133 ± 34 10,745 ± 3,144 26 ± 5 57 + 17 Monomer- Dimer hybrid Aranesp ®Subcutaneous 20 0.54  83 ± 11 5390 ± 747 22 ± 2 53 + 8 

Example 29 Intravenous Administration of EPOFc Monomer-Dimer Hybrid

To compare serum concentrations of known erythropoietin agents withEPOFc monomer-dimer hybrids, EPOFc monomer-dimer hybrid, Aranesp®(darbepoetin alfa), and Epogen® (epoetin alfa), neither of which is achimeric fusion protein, were administered intravenously to differentmonkeys and the serum concentration of both was measured over time.

Cynomolgus monkeys (n=3 per group) were injected intravenously with0.025 mg/kg EpoFc monomer-dimer hybrid. Blood samples were collectedpredose and at times up to 144 hours post dose. Serum was prepared fromthe blood and stored frozen until analysis by ELISA (Human EpoQuantikine Immunoassay) (R & D Systems, Minneapolis, Minn.).Pharmacokinetic parameters were determined using WinNonLina software(Pharsight, Mountainview, Calif.).

The results indicated the serum concentration versus time (AUC) of EPOFcmonomer-dimer hybrid was greater than the concentrations of eitherEpogen® (epoetin alfa) or Aranesp® (darbepoetin alfa), even though themonkeys received larger molar doses of both Epogen® (epoetin alfa) andAranesp® (darbepoetin alfa) (Table 7) (FIG. 13).

TABLE 7 Dose Dose Cmax AUC T_(1/2) Route (μg/kg) (nmol/kg) (ng/mL) (ng ·hr · mL⁻¹) (hr) EpoFc Intravenous 25 0.3 622 ± 110 18,913 ± 3,022 23 ± 1Monomer- Dimer hybrid Aranesp ® Intravenous 20 0.54 521 ± 8  10,219 ±298   20 ± 1 Epogen Intravenous 20 0.66 514 ± 172 3936 ± 636  6.3 ± 0.6

Example 30 Alternative Purification of EpoFc Monomer-Dimer Hybrid

Yet another alternative for purifying EPO-Fc is described herein. Amixture containing Fc, EpoFc monomer-dimer hybrid, and EpoFc dimer wasapplied to a Protein A Sepharose column (Amersham, Uppsala, Sweden). Themixture was eluted according to the manufacturer's instructions. TheProtein A Sepharose eluate, containing the mixture was buffer exchangedinto 50 mM Tris-Cl (pH 8.0). The protein mixture was loaded onto an 8 mLMimetic Red 2 XL column (ProMetic Life Sciences, Inc., Wayne, N.J.) thathad been equilibrated in 50 mM Tris-Cl (pH 8.0). The column was thenwashed with 50 mM Tris-Cl (pH 8.0); 50 mM NaCl. This step removed themajority of the Fc. EpoFc monomer-dimer hybrid was specifically elutedfrom the column with 50 mM Tris-Cl (pH 8.0); 400 mM NaCl. EpoFc dimercan be eluted and the column regenerated with 5 column volumes of 1 MNaOH. Eluted fractions from the column were analyzed by SDS-PAGE (FIG.14).

Example 31 Cloning of Igx Signal Sequence-Fc Construct for MakingUntapped Fc Alone

The coding sequence for the constant region of IgG1 (EU #221-447; the Fcregion) was obtained by PCR amplification from a leukocyte cDNA library(Clontech, CA) using the following primers:

rcFc-F (SEQ ID NO: 82) 5′- GCTGCGGTCGACAAAACTCACACATGCCCACCGTGCCCAGCTCCGGAACTCCTGGGCGGACCGTCAGTC -3′ rcFc-R (SEQ ID NO: 83)5′- ATTGGAATTCTCATTTACCCGGAGACAGGGAGAGGC -3′

The forward primer adds three amino acids (AAV) and a SalI cloning sitebefore the beginning of the Fc region, and also incorporates a BspEIrestriction site at amino acids 231-233 and an RsrII restriction site atamino acids 236-238 using the degeneracy of the genetic code to preservethe correct amino acid sequence (EU numbering). The reverse primer addsan EcoRI cloning site after the stop codon of the Fc. A 25 μl PCRreaction was carried out with 25 pmol of each primer using Expand HighFidelity System (Boehringer Mannheim, Indianapolis, Ind.) according tothe manufacturer's standard protocol in a MJ Thermocycler using thefollowing cycles: 94° C. 2 minutes; 30 cycles of (94° C. 30 seconds, 58°C. 30 seconds, 72° C. 45 seconds), 72° C. 10 minutes. The expected sizedband (˜696 bp) was gel purified with a Gel Extraction kit (Qiagen,Valencia Calif.), and cloned into pGEM T-Easy (Promega, Madison, Wis.)to produce an intermediate plasmid pSYN-Fc-001 (pGEM T-Easy/Fc).

The mouse Igκ signal sequence was added to the Fc CDS using thefollowing primers:

rc-Igk sig seq-F: (SEQ ID NO: 100)5′-TTTAAGCTTGCCGCCACCATGGAGACAGACACACTCCTGCTATGGGTACTGCTGCTCTGGGTTCCAGGTTCCACTGGTGACAAAACT CACACATGCCCACCG -3′Fc-noXma-GS-R: (SEQ ID NO: 101) 5′- GGTCAGCTCATCGCGGGATGGG -3′Fc-noXma-GS-F: (SEQ ID NO: 102) 5′- CCCATCCCGCGATGAGCTGACC -3′

The rc-IgK signal sequence-F primer adds a HindIII restriction site tothe 5′ end of the molecule, followed by a Kozak sequence (GCCGCCACC)(SEQ ID NO: 103) followed by the signal sequence from the mouse IgKlight chain, directly abutted to the beginning of the Fc sequence(EU#221). The Fc-noXma-GS-F and -R primers remove the internal Xmal sitefrom the Fc coding sequence, using the degeneracy of the genetic code topreserve the correct amino acid sequence. Two 25 μl PCR reactions werecarried out with 25 pmol of either rc-Igκ signal sequence-F andFc-noXma-GS-R or Fc-noXma-GS-F and rcFc-R using Expand High FidelitySystem (Boehringer Mannheim, Indianapolis, Ind.) according to themanufacturer's standard protocol in a MJ Thermocycler. The firstreaction was carried out with 500 ng of leukocyte cDNA library (BDBiosciences Clontech, Palo Alto, Calif.) as a template using thefollowing cycles: 94° C. 2 minutes; 30 cycles of (94° C. 30 seconds, 55°C. 30 seconds, 72° C. 45 seconds), 72° C. 10 minutes. The secondreaction was carried out with 500 ng of pSYN-Fc-001 as a template(above) using the following cycles: 94° C. 2 minutes; 16 cycles of (94°C. 30 seconds, 58° C. 30 seconds, 72° C. 45 seconds), 72° C. 10 minutes.The expected sized bands (˜495 and 299 bp, respectively) were gelpurified with a Gel Extraction kit (Qiagen, Valencia Calif.), thencombined in a PCR reaction with 25 pmol of rc-Igκ signal sequence-F andrcFc-R primers and run as before, annealing at 58° C. and continuing for16 cycles. The expected sized band (˜772 bp) was gel purified with a GelExtraction kit (Qiagen, Valencia Calif.) and cloned into pGEM T-Easy(Promega, Madison, Wis.) to produce an intermediate plasmid pSYN-Fc-007(pGEM T-Easy/Igk sig seq-Fc). The entire Igκ signal sequence-Fc cassettewas then subcloned using the HindIII and EcoRI sites into either thepEE6.4 (Lonza, Slough, UK) or pcDNA3.1 (Invitrogen, Carlsbad, Calif.)mammalian expression vector, depending on the system to be used, togenerate pSYN-Fc-009 (pEE6.4/Igκ sig seq-Fc) and pSYN-Fc-015 (pcDNA3/Igκsig seq-Fc).

Example 32 Cloning of lgic Signal Sequence-Fc N297A Construct for MakingUntamed Fc N297A alone

In order to mutate Asn 297 (EU numbering) of the Fc to an Ala residue,the following primers were used:

N297A-F (SEQ ID NO: 104) 5′- GAGCAGTACGCTAGCACGTACCG -3′ N297A-R(SEQ ID NO: 105) 5′- GGTACGTGCTAGCGTACTGCTCC -3′

Two PCR reactions were carried out with 25 pmol of either rc-Igκ signalsequence-F and N297A-R or N297A-F and rcFc-R using Expand High FidelitySystem (Boehringer Mannheim, Indianapolis, Ind.) according to themanufacturer's standard protocol in a MJ Thermocycler. Both reactionswere carried out using 500 ng of pSYN-Fc-007 as a template using thefollowing cycles: 94° C. 2 minutes; 16 cycles of (94° C. 30 seconds, 48°C. 30 seconds, 72° C. 45 seconds), 72° C. 10 minutes. The expected sizedbands (˜319 and 475 bp, respectively) were gel purified with a GelExtraction kit (Qiagen, Valencia Calif.), then combined in a PCRreaction with 25 pmol of rc-Igκ signal sequence-F and rcFc-R primers andrun as before, annealing at 589 C and continuing for 16 cycles. Theexpected sized band (˜772 bp) was gel purified with a Gel Extraction kit(Qiagen, Valencia Calif.) and cloned into pGEM T-Easy (Promega, Madison,Wis.) to produce an intermediate plasmid pSYN-Fc-008 (pGEM T-Easy/Igκsig seq-Fc N297A). The entire Igκ signal sequence-Fc alone cassette wasthen subcloned using the HindIII and EcoRI sites into either the pEE6.4(Lonza, Slough, UK) or pcDNA3.1 (Invitrogen, Carlsbad, Calif.) mammalianexpression vector, depending on the system to be used, to generatepSYN-Fc-010 (pEE6.4/IgK sig seq-Fc N297A) and pSYN-Fc-016 pcDNA3/IgK sigseq-Fc N297A).

These same N297A primers were also used with rcFc-F and rcFc-R primersand pSYN-Fc-001 as a template in a PCR reaction followed by subcloningas indicated above to generate pSYN-Fc-002 (pGEM T Easy/Fc N297A).

Example 33 Cloning Of EpoFc and Fc into Single Plasmid for Double GeneVectors for Making EpoFc Wildtype or N297a Monomer-Dimer Hybrids, andExpression

An alternative to transfecting the EpoFc and Fc constructs on separateplasmids is to clone them into a single plasmid, also called a doublegene vector, such as used in the Lonza Biologics (Slough, UK) system.The RsrII/EcoRI fragment from pSYN-Fc-002 was subcloned into thecorresponding sites in pEE12.4 (Lonza Biologics, Slough, UK) accordingto standard procedures to generate pSYN-Fc-006 (pEE12.4/Fc N297Afragment). The pSYN-EPO-004 plasmid was used as a template for a PCRreaction using Epo-F primer from Example 25 and the following primer:

EpoRsr-R: (SEQ ID NO: 106) 5′- CTGACGGTCCGCCCAGGAGTTCCGGAGCTGGGCACGGTGGGCATG TGTGAGITTIGTCGACCGCAGCGG -3′

A PCR reaction was carried out using Expand High Fidelity System(Boehringer Mannheim, Indianapolis, Ind.) according to themanufacturer's standard protocol in a MJ Thermocycler as indicatedabove, for 16 cycles with 552C annealing temperature. The expected sizedband (˜689 bp) was gel purified with a Gel Extraction kit (Qiagen,Valencia Calif.) and cloned into pSYN-Fc-006 using the HindIII/RsrIIrestriction sites, to generate pSYN-EPO-005 (pEE12.4/EpoFc N297A). Thedouble gene vector for the EpoFc N297A monomer-dimer hybrid was thenconstructed by cloning the NotI/BamHI fragment from pSYN-Fc-010 into thecorresponding sites in pSYN-EPO-005 to generate pSYN-EPO-008(pEE12.4-6.4/EpoFc N297A/Fc N297A).

The wild type construct was also made by subcloning the wild type Fcsequence from pSYN-Fc-001 into pSYN-EPO-005 using the RsrII and EcoRIsites, to generate pSYN-EPO-006 (pEE 12.4/EpoFc). The double gene vectorfor the EpoFc monomer-dimer hybrid was then constructed by cloning theNotI/BamHI fragment from pSYN-Fc-009 into the corresponding sites inpSYN-EPO-006 to generate pSYN-EPO-007 (pEE12.4-6.4/EpoFc/Fc).

Each plasmid was transfected into CHOK1SV cells and positive clonesidentified and adpated to serum-free suspension, as indicated in theLonza Biologics Manual for Standard Operating procedures (LonzaBiologics, Slough, UK), and purified as indicated for the othermonomer-dimer constructs.

Example 34 Cloning of Human IFNβFc, IFNβ-Fc N297a with Eight Amino AcidLinkers and Igk-Fc-6His Constructs (6×His tag Disclosed as SEQ ID NO:107)

10 ng of a human genomic DNA library from Clontech (BD BiosciencesClontech, Palo Alto, Calif.) was used as a template to isolate humanIFNβ with its native signal sequence using the following primers:

IFNβ-F H3/SbfI: (SEQ ID NO: 92) 5′- CTAGCCTGCAGGAAGCTTGCCGCCACCATGACCAACAAGTGTCTCCTC -3′ IFNβ-R (EFAG) Sal: (SEQ ID NO: 93)5′TTTGTCGACCGCAGCGGCGCCGGCGAACTCGTTTCGG AGGTAACCTGTAAG -3′

The reverse primer was also used to create an eight amino acid linkersequence (EFAGAAAV) (SEQ ID NO: 31) on the 3′ end of the human IFNβsequence. The PCR reaction was carried out using the Expand HighFidelity System (Boehringer Mannheim, Indianapolis, Ind.) according tothe manufacturer's standard protocol in a Rapid Cycler thermocycler(Idaho Technology, Salt Lake City, Utah). A PCR product of the correctsize (˜607 bp) was gel purified using a Gel Extraction kit (Qiagen;Valencia, Calif.), cloned into TA cloning vector (Promega, Madison,Wis.) and sequenced. This construct was named pSYN-IFNβ-002.pSYN-IFNβ-002 was digested with SbfI and SalI and cloned into pSP72(Promega) at PstI and SalI sites to give pSYN-IFNβ-005.

Purified pSYN-Fc-001 (0.6 μg) was digested with SalI and EcoRI andcloned into the corresponding sites of pSYN-IFNβ-005 to create theplasmid pSYN-IFNβ-006 which contains human IFNβ linked to human Fcthrough an eight amino acid linker sequence. pSYN-IFNβ-006 was thendigested with SbfI and EcoRI and the full-length IFNβ-Fc sequence clonedinto the PstI and EcoRI sites of pEDdC.sig to create plasmidpSYN-IFNβ-008.

pSYN-Fc-002 containing the human Fc DNA with a single amino acid changefrom asparagine to alanine at position 297 (N297A; EU numbering) wasdigested with BspEI and XmaI to isolate a DNA fragment of ˜365 bpcontaining the N297A mutation. This DNA fragment was cloned into thecorresponding sites in pSYN-IFNβ-008 to create plasmid pSYN-IFNβ-009that contains the IFNβ-Fc sequence with an eight amino acid linker andan N297A mutation in Fc in the expression vector, pED.dC.

Cloning of Igk signal sequence-Fc N297A-6His-(SEQ ID NO: 107). Thefollowing primers were used to add a 6×His tag (SEQ ID NO: 107) to the Cterminus of the Fc N297A coding sequence:

Fc GS-F: (SEQ ID NO: 94) 5′- GGCAAGCTTGCCGCCACCATGGAGACAGACACACTCC -3′Fc.6His-R: (SEQ ID NO: 95)5′- TCAGTGGTGATGGTGATGATGTTTACCCGGAGACAGGGAG -3′ Fc.6His-F(6xHis tag disclosed as SEQ ID NO: 107): (SEQ ID NO: 96) 5′-GGTAAACATCATCACCATCACCACTGAGAATTCC AATATCACTAGTGAA TTCG - 3′ Sp6 + T-R:(SEQ ID NO: 97) 5′- GCTATTTAGGTGACACTATAGAATACTCAAGC -3′

Two PCR reactions were carried out with 50 pmol of either Fc GS-F andFc.6His-R (6×His tag disclosed as SEQ ID NO: 107) or Fc.6His-F (6×Histag disclosed as SEQ ID NO: 107) and Sp6+T-R using the Expand HighFidelity System (Boehringer Mannheim, Indianapolis, Ind.) according tothe manufacturer's standard protocol in a MJ Thermocycler. Bothreactions were carried out using 500 ng of pSYN-Fc-008 as a template ina 50 μl reaction, using standard cycling conditions. The expected sizedbands (˜780 and 138 bp, respectively) were gel purified with a GelExtraction kit (Qiagen, Valencia Calif.), then combined in a 50 μl PCRreaction with 50 pmol of Fc GS-F and Sp6+T-R primers and run as before,using standard cycling conditions. The expected sized band (˜891 bp) wasgel purified with a Gel Extraction kit (Qiagen, Valencia Calif.) andcloned into pcDNA6 V5-His B using the HindIII and EcoRI sites togenerate pSYN-Fc-014 (pcDNA6/IgK sig seq-Fc N297A-6 His).

Example 35 Expression and Purification of IFNβFc, IFNβ-Fc N297Ahomodimer and IFNβ-Fc N297A Monomer-Dimer Hybrid

CHO DG44 cells were plated in 100 mm tissue culture dishes and grown toa confluency of 50%-60%. A total of 10 μg of DNA was used to transfect asingle 100 mm dish. For the homodimer transfection, 10 μg of thepSYN-FNβ-008 or pSYN-IFNβ-009 construct was used; for the monomer-dimerhybrid transfection, 8 μg of the pSYN-IFNβ-009+2 μg of pSYN-Fc-014construct was used. The cells were transfected using Superfecttransfection reagents (Oiagen, Valencia, Calif.) according to themanufacturer's instructions. 48 to 72 hours post-transfection, growthmedium was removed and cells were released from the plates with 0.25%trypsin and transferred to T75 tissue culture flasks in selection medium(MEM Alpha without nucleosides plus 5% dialyzed fetal bovine serum). Theselection medium for the monomer-dimer hybrid transfection wassupplemented with 5 μg/ml Blasticidin (Invitrogen, Carlsbad, Calif.).Selection was continued for 10-14 days until the cells began to growwell and stable cell lines were established. Protein expression wassubsequently amplified by the addition methotrexate: ranging from 10 to50 nM.

For all cell lines, approximately 2×10⁷ cells were used to inoculate 300ml of growth medium in a 1700 cm² roller bottle (Corning, Corning,N.Y.). The roller bottles were incubated in a 5% CO₂ incubator at 37° C.for approximately 72 hours. The growth medium was then exchanged with300 ml serum-free production medium (DMEM/F12 with 5 μg/ml humaninsulin). The production medium (conditioned medium) was collected everyday for 10 days and stored at 4° C. Fresh production medium was added tothe roller bottles after each collection and the bottles were returnedto the incubator. Prior to chromatography, the medium was clarifiedusing a Supor Cap-100 (0.8/0.2 μm) filter from Pall Gelman Sciences (AnnArbor, Mich.). All of the following steps were performed at 4° C. Theclarified medium was applied to Protein A Sepharose, washed with 5column volumes of 1×PBS (10 mM phosphate, pH 7.4, 2.7 mM KCl, and 137 mMNaCl), eluted with 0.1 M glycine, pH 2.7, and then neutralized with 1/10volume of 1 M Tris-HCl pH 8.0, 5 M NaCl. The homodimer proteins werefurther purified over a Superdex 200 Prep Grade sizing column run andeluted in 50 mM sodium phosphate pH 7.5, 500 mM NaCl, 10% glycerol.

The monomer-dimer hybrid protein was subject to further purificationsince it contained a mixture of IFNβFc N297A:IFNβFc N297A homodimer,IFNβFc N297A: Fc N297A His monomer-dimer hybrid, and Fc N297A His: FcN297A His homodimer. Material was applied to a Nickel chelating columnin 50 mM sodium phosphate pH 7.5, 500 mM NaCl. After loading, the columnwas washed with 50 mM imidazole in 50 mM sodium phosphate pH 7.5, 500 mMNaCl and protein was eluted with a gradient of 50-500 mM imidazole in 50mM sodium phosphate pH 7.5, 500 mM NaCl. Fractions corresponding toelution peaks on a UV detector were collected and analyzed by SDS-PAGE.Fractions from the first peak contained IFNβFc N297A: Fc N297A Hismonomer-dimer hybrid, while the second peak contained Fc N297A His: FcN297A His homodimer. All fractions containing the monomer-dimer hybrid,but no Fc homodimer, were pooled and applied directly to a Superdex 200Prep Grade sizing column, run and eluted in 50 mM sodium phosphate pH7.5, 500 mM NaCl, 10% glycerol. Fractions containing IFNβ-Fc N297A:FcN297A His monomer-dimer hybrids were pooled and stored at −80° C.

Example 36 Antiviral Assay for IFNβ Activity

Antiviral activity (IU/ml) of IFNβ fusion proteins was determined usinga CPE (cytopathic effect) assay. A549 cells were plated in a 96 welltissue culture plate in growth media (RPMI 1640 supplemented with 10%fetal bovine serum (FBS) and 2 mM L-glutamine) for 2 hours at 37° C., 5%CO₂. IFNβ standards and IFNβ fusion proteins were diluted in growthmedia and added to cells in triplicate for 20 hours at 37° C., 5% CO₂.Following incubation, all media was removed from wells,encephalomyocarditis virus (EMCV) was diluted in growth media and added(3000 pfu/well) to each well with the exception of control wells. Plateswere incubated at 37° C., 5% CO₂ for 28 hours. Living cells were fixedwith 10% cold trichloroacetic acid (TCA) and then stained withSulforhodamine B (SRB) according to published protocols (Rubinstein etal. 1990, J. Natl. Cancer Inst. 82, 1113). The SRB dye was solubilizedwith 10 mM Tris pH 10.5 and read on a spectrophotometer at 490 nm.Samples were analyzed by comparing activities to a known standard curveranging from 10 to 0.199 IU/ml. The results are presented below in Table8 and demonstrate increased antiviral activity of monomer-dimer hybrids.

TABLE 8 INTERFERON BETA ANTIVIRAL ASSAY HOMODIMER V. MONOMER-DIMERHYBRID Antiviral Activity Protein (IU/nmol) Std dev IFNβ-Fc 8aa linkerhomodimer  4.5 × 10⁵ 0.72 × 10⁵ IFNβFc N297A 8aa linker homodimer 3.21 ×10⁵ 0.48 × 10⁵ IFNβFc N297A 8aa linker Fc His 12.2 × 10⁵   2 × 10⁵monomer-dimer hybrid

Example 37 Administration of IFNβFc Homodimer and Monomer-Dimer Hybridwith an Eight Amino Acid Linker to Cvnomolqus Monkeys

For pulmonary administration, aerosols of either IFNβFc homodimer orIFNβFc N297A monomer-dimer hybrid proteins (both with the 8 amino acidlinker) in PBS, pH 7.4, 0.25% HSA were created with the Aeroneb Pro™(AeroGen, Mountain View, Calif.) nebulizer, in-line with a Bird Mark 7Arespirator, and administered to anesthetized naïve cynomolgus monkeysthrough endotracheal tubes (approximating normal tidal breathing). Bloodsamples were taken at various time points, and the amount ofIFNβ-containing protein in the resulting serum was quantitated using ahuman IFNβ Immunoassay (Biosource International, Camarillo, Calif.).Pharmacokinetic parameters were calculated using the software WinNonLin.Table 9 presents the results of cynomolgus monkeys treated with IFNβFcN297A monomer-dimer hybrid or IFNβFc homodimer.

TABLE 9 ADMINISTRATION OF IFNβFC N297A MONOMER-DIMER HYBRID AND IFNβFCHOMODIMER TO MONKEYS Approx. Deposited Dose¹ C_(max) AUC t_(1/2) t_(1/2)avg Protein Monkey # Route (μg/kg) (ng/ml) (ng · hr · mL⁻¹) (hr) (hr)IFNβFc C07308 pulm 20 23.3 987.9 27.6 27.1 N297A C07336 pulm 20 22.4970.6 25.6 monomer- C07312 pulm 20 21.2 1002.7 28.0 dimer hybrid IFNβFcC07326 pulm 20 2.6 94.6 11.1 11.4 homodimer C07338 pulm 20 5.0 150.611.7 ¹Based on 15% deposition fraction of nebulized dose as determinedby gamma scintigraphy

The pharmacokinetics of IFNβFc with an 8 amino acid linker administeredto cynomolgus monkeys is presented in FIG. 15. The figure compares theIFNβFc homodimer with the IFNβFc N297A monomer-dimer hybrid in monkeysafter administration of a single pulmonary dose. Significantly higherserum levels were obtained in monkeys treated with the monomer-dimerhybrid compared to the homodimer.

Serum samples were also analyzed for neopterin levels (a biomarker ofIFNβ activity) using a neopterin immunoassay (MP Biomedicals,Orangeburg, N.Y.). The results for this analysis are shown in FIG. 16.The figure compares neopterin stimulation in response to the IFNβ-Fchomodimer and the IFNβ-Fc N297A monomer-dimer hybrid. It can be seenthat significantly higher neopterin levels were detected in monkeystreated with IFNβ-Fc N297A monomer-dimer hybrid as compared to theIFNβ-Fc homodimer.

All numbers expressing quantities of ingredients, reaction conditions,and so forth used in the specification and claims are to be understoodas being modified in all instances by the term “about.” Accordingly,unless indicated to the contrary, the numerical parameters set forth inthe specification and attached claims are approximations that may varydepending upon the desired properties sought to be obtained by thepresent invention. At the very least, and not as an attempt to limit theapplication of the doctrine of equivalents to the scope of the claims,each numerical parameter should be construed in light of the number ofsignificant digits and ordinary rounding approaches.

All references cited herein are incorporated herein by reference intheir entirety and for all purposes to the same extent as if eachindividual publication or patent or patent application was specificallyand individually indicated to be incorporated by reference in itsentirety for all purposes. To the extent publications and patents orpatent applications incorporated by reference contradict the disclosurecontained in the specification, the specification is intended tosupercede and/or take precedence over any such contradictory material.

Many modifications and variations of this invention can be made withoutdeparting from its spirit and scope, as will be apparent to thoseskilled in the art. The specific embodiments described herein areoffered by way of example only and are not meant to be limiting in anyway. It is intended that the specification and examples be considered asexemplary only, with a true scope and spirit of the invention beingindicated by the following claims.

1. A chimeric protein comprising a first and second polypeptide chain,wherein said first chain comprises a biologically active molecule, andat least a portion of an immunoglobulin constant region and wherein saidsecond chain comprises at least a portion of an immunoglobulin constantregion without a biologically active molecule or immunoglobulin variableregion.
 2. The chimeric protein of claim 1, wherein said second chainfurther comprises an affinity tag.
 3. The chimeric protein of claim 2,wherein the affinity tag is a FLAG tag.
 4. The chimeric protein of claim1, wherein the portion of an immunoglobulin is an Fc fragment. 5.-31.(canceled)
 32. A chimeric protein comprising a first and secondpolypeptide chain a) wherein said first chain comprises a biologicallyactive molecule, at least a portion of an immunoglobulin constantregion, and a first domain having at least one specific binding partner;and b) wherein said second chain comprises at least a portion of animmunoglobulin without a biologically active molecule or immunoglobulinvariable region and further comprising a second domain said seconddomain being a specific binding partner of said first domain.
 33. Thechimeric protein of claim 32, wherein said second chain furthercomprises an affinity tag.
 34. The chimeric protein of claim 33, whereinthe affinity tag is a FLAG tag.
 35. The chimeric protein of claim 32,wherein the portion of an immunoglobulin is an Fe fragment. 36.-64.(canceled)
 65. A method of making a biologically active chimeric proteincomprising: a) transfecting a cell with a first DNA construct comprisinga DNA molecule encoding a polypeptide comprising a biologically activemolecule operatively linked to a second DNA molecule encoding at least aportion of an immunoglobulin constant region; b) transfecting the cellwith a second. DNA construct comprising a DNA molecule encoding apolypeptide comprising at least a portion of an immunoglobulin constantregion without a biologically active molecule or variable region of animmunoglobulin; c) culturing the cell under conditions such that thepolypeptide encoded by said first DNA construct and said second DNAconstruct is expressed; and d) isolating dimers of a) and b) from saidtransfected cell.
 66. The method of claim 65, wherein said portion of animmunoglobulin constant region is an FcRn binding partner.
 67. Themethod of claim 65, wherein the biologically active molecule is apolypeptide.
 68. The method of claim 65, wherein the biologically activemolecule is interferon. 69.-71. (canceled)
 72. The method of claim 65,wherein the biologically active molecule is a viral fusion inhibitor, agrowth factor, or a hormone.
 73. (canceled)
 74. (canceled)
 75. Themethod of claim 65, wherein the biologically active molecule comprises aclotting factor.
 76. The method of claim 75, wherein the clotting factoris Factor VII or Factor VIIa.
 77. The method of claim 75, wherein theclotting factor is Factor IX. 78.-84. (canceled)
 85. The method of claim65, wherein the dimers are isolated by chromatography.
 86. The method ofclaim 65, wherein the cell is a eukaryotic cell.
 87. The method of claim86, wherein the eukaryotic cell is a CHO cell.
 88. (canceled) 89.(canceled)
 90. A method of treating a subject with a disease orcondition comprising administering the chimeric protein of claim 1 tothe subject, such that said disease or condition is treated.
 91. Themethod of claim 90, wherein said chimeric protein is administeredintravenously, subcutaneously, orally, buccally, sublingually, nasally,parenterally, rectally, vaginally or via a pulmonary route. 92.-98.(canceled)
 99. The method of claim 90, wherein said disease or conditionis a hemostatic disorder. 100.-130. (canceled)
 131. A method of treatinga disease or condition in a subject comprising administering thechimeric protein of claim 32 to said subject. 132.-153. (canceled) 154.A method of making a chimeric protein comprising an Fc fragment of animmunoglobulin linked to a biologically active molecule, said methodcomprising a) transfecting a cell with a DNA construct comprising a DNAsequence encoding an Fc fragment of an immunoglobulin and a second DNAsequence encoding intein; b) culturing said cell under conditions suchthat the Fc fragment and intein is expressed; c) isolating said Fcfragment and intein from said cell; d) chemically synthesizing abiologically active molecule having an N terminal Cys; e) reacting theisolated intein Fc of c) with MESNA to generate a C terminal thio-ester;f) reacting the biologically active molecule of d) with the Fc of e) tomake a chimeric protein comprising an Fc linked to a biologically activemolecule. 155.-159. (canceled)
 160. A method of isolating amonomer-dimer hybrid from a mixture, where the mixture comprises, a) thechimeric protein of claim 1; b) a dimer comprising a first and secondpolypeptide chain, wherein the first and second chains both comprise abiologically active molecule, and at least a portion of animmunoglobulin constant region; c) a portion of an immunoglobulinconstant region; said method comprising 1) contacting the mixture with adye ligand linked to a solid support under suitable conditions such thatboth the chimeric protein and the dimer bind to the dye ligand; 2)removing the unbound portion of an immunoglobulin constant region; 3)altering the suitable conditions of 1) such that the binding between thechimeric protein and the dye ligand linked to the solid support isdisrupted; 4) isolating the chimeric protein.
 161. The method of claim160, wherein the portion of an immunoglobulin is an Fc fragment. 162.The method of claim 160, wherein the dye-ligand is a bio-mimeticmolecule. 163.-194. (canceled)
 195. The method of claim 75, wherein theclotting factor is Factor VIII or Factor VIIIa.
 196. A method of makinga biologically active chimeric protein comprising: a) transfecting afirst cell with a first DNA construct comprising a DNA molecule encodinga polypeptide comprising a biologically active molecule operativelylinked to a second DNA molecule encoding at least a portion of animmunoglobulin constant region; b) transfecting a second cell with asecond DNA construct comprising a DNA molecule encoding a polypeptidecomprising at least a portion of an immunoglobulin constant regionwithout a biologically active molecule or variable region of animmunoglobulin; c) culturing the cell of a) and b) under conditions suchthat the polypeptide encoded by said first DNA construct and said secondDNA construct is expressed; and d) isolating dimers of a) and b) fromsaid transfected cells.